Tagron, excellent analysis.
Indeed, a crucial element of the causes leading to the crash is probably the "special" approach procedure planned by the crew, which was probably not conducted by the book.
It is highly likely that the procedure planned by TU-154 crew was the same or similar to that of the JAK-40 crew.
From the report page. 169:
... is also confirmed by the interview with the YAK-40 crew, who stated that they were preparing to land using the markers with GPS monitoring
So they planned to do NDB approach monitored by GPS. In fact, according to statements of the Jak-40 PIC, it was rather a GPS approach with additionally NDB guiding. The PIC acknowledged that - beause they thought the markers were malfunctioning - used GPS alone shortly before landing!
As you properly observed, the GPS waypoints entered in the FMS didnt match the fix points of the NDB chart:
Instead of runway treshhold, ARP was used. Additionally, the waypoint for the outer marker was not converted to WGS-84 and thus erroneous. The middle marker wasnt entered at all.
So, they monitored NDB approach by matching the plates fix points with supposedly corresponding waymarkers on the GPS.
The problem was, the reference points werent matching at all.
Conclusion:
Jak-40 were lucky not to crash as well.