As a PythonX operator, Looking at your list of problems, the majority of these issues is based on rounding errors in the NC files with the cuts running down the length of the part. There is usually one number in the y dimension that is off by .01mm.
Doesn't matter what the drafting program is used, it happens with all of them. Our Python X at work has been a learning curve. There is a lot of things that you can do that they say you can't. We have blown ther minds with some of the stuff we are doing with it.
98% of the file issues is operator error.
PythonX support can help with machine settings to resolve these issues.
I noticed one part looks like a WT. The Python will not cut a Tee from a WT file. There is a work around for that though.
The machine will process flat bar. We do it at least once a week.
The numbering issue is a problem with Advance Steel on the placement. I change the location of the part numbers on a daily basis. Sometimes as many a few hundred a day, depends on how many beams are processed. I have a text file with proven x,y positions saved for different material sizes.