There are currently 50 instances I detected of the situation I described in the OP. Places where the same coordinates are used on two routes, either intersecting or as part of a concurrency, but one route's waypoint is hidden while the other is visible. Thoughts?
ERROR: hidden waypoint colocated with visible, sct.e5gla +M74 (55.851204,-4.272523) and sct.e5 M8/M74 (55.851204,-4.272523)
ERROR: hidden waypoint colocated with visible, sct.e16 +M74 (55.851204,-4.272523) and sct.e5 M8/M74 (55.851204,-4.272523)
ERROR: hidden waypoint colocated with visible, bel.e19 +N133 (51.35364,4.630265) and bel.a001 *N133 (51.35364,4.630265)
ERROR: hidden waypoint colocated with visible, che.e27 +11(A16) (47.351545,7.366934) and che.a016 11 (47.351545,7.366934)
ERROR: hidden waypoint colocated with visible, swe.e45 Avv (67.330253,21.078579) and swe.e10 +X34 (67.330253,21.078579)
ERROR: hidden waypoint colocated with visible, cze.e55 +52(D8) (50.527479,13.999629) and cze.d008 52 (50.527479,13.999629)
ERROR: hidden waypoint colocated with visible, aut.e55 +A7/S10 (48.356257,14.460582) and aut.a007 S10 [alt: ['+B125']] (48.356257,14.460582)
ERROR: hidden waypoint colocated with visible, aut.e461 +S1/S2 (48.285863,16.514103) and aut.s001wie 36 [alt: ['+B8']] (48.285863,16.514103)
ERROR: hidden waypoint colocated with visible, esp.a001vit NC/PV (42.93272,-2.227993) and esp.e5bea +NC/PV (42.93272,-2.227993)
ERROR: hidden waypoint colocated with visible, esp.b030 4 (41.491912,2.095385) and esp.e15 +4(B30) (41.491912,2.095385)
ERROR: hidden waypoint colocated with visible, fra.a006a +N186 (48.756189,2.334294) and fra.e15 N186 [alt: ['+A86']] (48.756189,2.334294)
ERROR: hidden waypoint colocated with visible, sct.m008 +M74 (55.851204,-4.272523) and sct.e5 M8/M74 (55.851204,-4.272523)
ERROR: hidden waypoint colocated with visible, sct.m074 +M8 (55.851204,-4.272523) and sct.e5 M8/M74 (55.851204,-4.272523)
ERROR: hidden waypoint colocated with visible, eng.a001m +X27 (54.261565,-1.517572) and eng.e15 *B6285 (54.261565,-1.517572)
ERROR: hidden waypoint colocated with visible, eng.a001m +X28 (54.300633,-1.567305) and eng.e15 *A684 (54.300633,-1.567305)
ERROR: hidden waypoint colocated with visible, eng.a5080 M62(4) (53.405995,-2.89624) and eng.e20liv +M62(4) (53.405995,-2.89624)
ERROR: hidden waypoint colocated with visible, ita.ra001 +ViaMic (44.519023,11.371815) and ita.e45 ViaMic (44.519023,11.371815)
ERROR: hidden waypoint colocated with visible, pol.a002min 541 (52.197875,21.775675) and pol.e30 +541(A2) (52.197875,21.775675)
ERROR: hidden waypoint colocated with visible, pol.a004 581 (50.093564,22.058895) and pol.e40 +581(A4) (50.093564,22.058895)
ERROR: hidden waypoint colocated with visible, pol.s011 +270 (52.345722,16.754751) and pol.s005poz 201 (52.345722,16.754751)
ERROR: hidden waypoint colocated with visible, svk.d001 187 [alt: ['+D3']] (49.225593,18.608887) and svk.e50 +D1/D3 (49.225593,18.608887)
ERROR: hidden waypoint colocated with visible, svk.d003 0 [alt: ['D1']] (49.225593,18.608887) and svk.e50 +D1/D3 (49.225593,18.608887)
ERROR: hidden waypoint colocated with visible, tur.o005 16 (40.28974,29.025192) and tur.e90 +16(O5) (40.28974,29.025192)
ERROR: hidden waypoint colocated with visible, tur.o020 +6 (39.786824,32.742562) and tur.e90 6(O20) (39.786824,32.742562)
ERROR: hidden waypoint colocated with visible, tur.o022 O5 (40.28974,29.025192) and tur.e90 +16(O5) (40.28974,29.025192)
ERROR: hidden waypoint colocated with visible, ct.us007 US1 (41.118111,-73.419893) and ct.us001 +US7 (41.118111,-73.419893)
ERROR: hidden waypoint colocated with visible, ms.us078 +Fut269 (34.87896,-89.724784) and ms.i022futtup Fut269 (34.87896,-89.724784)
ERROR: hidden waypoint colocated with visible, co.us087 I-25(137) [alt: ['+137(I-25)']] (38.78321,-104.788091) and co.i025 +137 (38.78321,-104.788091)
ERROR: hidden waypoint colocated with visible, me.me170 StaFacRd (45.421144,-68.137025) and me.me169 +x0StaFacRd (45.421144,-68.137025)
ERROR: hidden waypoint colocated with visible, nv.nv599 JonBlvd (36.231154,-115.224974) and nv.us095buslsv +NV596 (36.231154,-115.224974)
ERROR: hidden waypoint colocated with visible, oh.oh043 +x240 (41.461389,-81.642509) and oh.oh014 AetAve (41.461389,-81.642509)
ERROR: hidden waypoint colocated with visible, oh.oh066 +x170 (41.288203,-84.361152) and oh.oh015 FortSt (41.288203,-84.361152)
ERROR: hidden waypoint colocated with visible, oh.oh328 +y91 (39.399007,-82.372897) and oh.oh056 LauRunRd (39.399007,-82.372897)
ERROR: hidden waypoint colocated with visible, aze.ah081 +X187946 (39.869235,48.232641) and aze.e002 Mur (39.869235,48.232641)
ERROR: hidden waypoint colocated with visible, bc.bc001 +x4 (49.227183,-122.81996) and bc.tchmai 44A (49.227183,-122.81996)
ERROR: hidden waypoint colocated with visible, chnnx.g70 +G22_W (35.591017,106.306715) and chnnx.g22 G70_W (35.591017,106.306715)
ERROR: hidden waypoint colocated with visible, chngx.g72 +G65/G76 (25.280441,110.158281) and chngx.g65 G72_E (25.280441,110.158281)
ERROR: hidden waypoint colocated with visible, irn.f001 R49_Man (36.730974,49.418435) and irn.ah008 +F1 (36.730974,49.418435)
ERROR: hidden waypoint colocated with visible, kor.ex065 7 (35.553737,129.249344) and kor.ah006 +7(Ex65) (35.553737,129.249344)
ERROR: hidden waypoint colocated with visible, kor.ex065och 10 (35.783006,129.424438) and kor.ah006 +10(Ex65) (35.783006,129.424438)
ERROR: hidden waypoint colocated with visible, kor.ex065gan 31 (37.512245,129.095535) and kor.ah006 +31(Ex65) (37.512245,129.095535)
ERROR: hidden waypoint colocated with visible, svk.i002 PanCes_N (48.131805,17.104812) and svk.e58 +1A(D1) (48.131805,17.104812)
ERROR: hidden waypoint colocated with visible, in.in003 +X00 (39.802074,-85.44548) and in.us040 *IN3 (39.802074,-85.44548)
ERROR: hidden waypoint colocated with visible, idn.ah002 +266 (-6.898735,108.880091) and idn.jtkp 266 (-6.898735,108.880091)
ERROR: hidden waypoint colocated with visible, bgr.ii066 +A4 (42.181405,25.246625) and bgr.a004 *II66 [alt: ['+N66']] (42.181405,25.246625)
ERROR: hidden waypoint colocated with visible, nl.nl430 +Goo/Yah (51.31232,-56.708475) and nl.nl430 MisCove (51.31232,-56.708475)
ERROR: hidden waypoint colocated with visible, ca.ca014trknew CA14 (34.335955,-118.508025) and ca.ca014 +CA14Trk (34.335955,-118.508025)
ERROR: hidden waypoint colocated with visible, fl.fl200 +X008(US301) (29.7613,-82.141685) and fl.us301 CR1469/1471 (29.7613,-82.141685)
ERROR: hidden waypoint colocated with visible, az.us066hiskin +Coc/Yav (35.507566,-113.183813) and az.az066 Coc/Yav (35.507566,-113.183813)
ERROR: hidden waypoint colocated with visible, mo.us066hisstl FR144 (37.192801,-93.542061) and mo.mo266 +X01 (37.192801,-93.542061)