My understanding is that the membrane system is a LP output, so the output from the membrane is subjected to the same filtration in the compressor that any other air would. Am I off track here?
Yes. Most compressors do not output o2 clean air. "Any other air" gets filtered to Grade-E levels for regular scuba use. To be compatible with o2 clean tanks, it needs to be further filtered to Mod Grade-E levels.
Half the reason shops go to Membrane systems (which cost a lot more than partial pressure blending setups) is to avoid the need for o2 clean tanks, since nothing comes out over 40%. The membrane merely takes regular air and filters out some of the nitrogen, so the resulting gas has a higher percentage of 02.