It does seem like with the fabric install, there are several ways to "skin a cat".
I used the build manual to give me some direction as for as how the pieces of fabric should go, but for the actual process, I pretty much followed the polyfiber manual and had good results.
I have seen some deviation from the manual on videos. I think it's like anything else. People who do this kind of work will find ways to get better, easier results and sometimes that will be slightly different from other instructions.
https://www.youtube.com/watch?v=sk-vaAxd2eE
The girl on this series of youtube videos does amazing work.
One tip that I used which deviated from the manual, was her tip of diluting the poly tak 50/50 with MEK. She dilutes, and then paints 2 coats on, lets it dry, and the then lays the fabric down. She then brushes over the fabric with the 50/50. This activates the painted on glue and really gets a good soak through the fabric.
This was a game changer for me since before using this method, it seems like it was a race to beat the drying polytak glue, which resulted in clumpy glue and areas where the fabric didn't adhere well, kind of like you describe.
Might give this technique a shot.....