This is a straw man argument.
There is substitutability in the assumptions. What you have always failed to recognize is that substitutability is little help when dealing with mutating through a sequence. What you have also failed to recognize is when dealing with populations variation to those populations is restricted by the time it takes for fixation to occur.
Lynch’s assumption of equal substitutability is not correct and from your first statement I think you agree with this.
If we want to get a better idea on how close Behe’s assumption is to reality we have a lot more studies available then those cited in an 18 year old paper.
The bigger question is how after 18 years is there no paper that shows gene duplication and divergence is a viable mechanism based on population genetic mathematics? There is also no paper that shows how any mechanism explains life’s diversity based on population genetics mathematics.
At some point without an ideological axe to grind someone might question if the universal common descent king has no clothes and stop the generation of papers that assume it is true