your response perhaps shows a misunderstanding, that there is some separate BSDL for 1149.1 vs. 1149.6. This may directly identify that there is a general knowledge gap around these standards which prevent providing customers useful information in IEEE compliant form. IEEE 1149.6 is a layer on top of 1149.1. The rules for BSDL come from 1149.1 and then extensions are added to support 1149.6. The very BSDLs you point to are the ones which are failing compilation. Altera, nor any other vendor, offer separate BSDLs one for 1149.1 and one for 1149.6 so the idea "these 1149.6 might work" is incorrect. This IS the compilation of a3cu100bb23c.bsdl it has no other form provided by Altera.
iBSDL - Intellitech BSDL Compiler Version 14.22
Copyright (C) 1993-2026 Intellitech Corp. All rights reserved.
ERROR: Associated port CDRCLKOUT_GTSL1A_CH2n was found in a PORT_GROUPING attribute. Associated ports, the second
port in a PORT_GROUPING statement can only be in the boundary register when the function
in the BOUNDARY_REGISTER attribute is OBSERVE_ONLY. One solution would be to remove CDRCLKOUT_GTSL1A_CH2n
from the PORT_GROUPING attribute. ( IEEE Std 1149.1 Rule B.8.8.3 d)
ERROR: Associated port REFCLK_GTSL1A_CH1n was found in a PORT_GROUPING attribute. Associated ports, the second
port in a PORT_GROUPING statement can only be in the boundary register when the function
in the BOUNDARY_REGISTER attribute is OBSERVE_ONLY. One solution would be to remove REFCLK_GTSL1A_CH1n
from the PORT_GROUPING attribute. ( IEEE Std 1149.1 Rule B.8.8.3 d)