It doesn't vary much but the answer is yes. However, keep in mind that traces for digital signals on various C64 boards pretty much all have the same width and the same copper thickness so the variation isn't very big.
The idea is, compared to today's computer motherboards or even those of early 90's Amiga and PC computers, the traces in the C64 are considerably larger and were built with much less attention to the parasitic capacitance and inductance. Consequently a C64 board made by Commodore has a much lower bandwidth limit than anything built today. At the same time, these bulky traces do act as RF noise filters.
Watch for the presence or absence of R42 and C204.I noticed that the dodgy Winbond W27C512 EEPROM PLA substitute in one of the three 250407 variants I tested actually seemed to work ok. However all the other boards didn't go so well.
You're not specifying what the components are but I suspect this still revolves around R42 and C204.I noticed that on the 2 Ku style mainboards I have they have added in extra components at the factory that are different from each other when viewed side by side.....
Were they trying to custom match the impedace load to PLA chip used?
Maybe the very early PLA chips exhibited some undesirable behaviour.
The PLA's currently in these KU boards are not the original ones but later 1986 dated PLA's.
The very first PLAs installed in C64 had a latency of 38ns, give or take. As soon as Commodore starting making their own in-house MOS 906114-01, the latency dropped and proper access to DRAM required a slowing down of the CASRAM signal. The was done with the above 2 parts.