Well PN does as good a job at turning clipped peaks into something resembling normal soundwaves as you can expect. I use it on all my tracks.
It really doesn’t matter what you use to normalise gain, unless you have tackled the clipping with something like PN, the clipping stays. Normalising only sets the volume to a preset level. But a clipped peak stays a clipped peak.
Best obviously is to have non-clipped material to start with (like you did with your vinyls, good job).
FLAC is usually not a root format. There are (as far as I know) no sound engineers that will master to FLAC. So FLAC is always the result of some sort of processing. And if you don’t know the root format was 24-bit, then it really doesn’t mean much that the FLAC is 24-bit, imho.
A professionally mastered track at 44.1/16-bit (CD-qaulity) without clipping will suffice as root format for going to 320MP3 without any problem.
24-bit to 16-bit conversion is something that can be done pretty well with decent DAW software, but might not be such a good idea without the proper tools (software and hardware).
Just my two cents.
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