Every pc soundcard resample to 44,1kHz (or higher but fixed)? I only know that in the past (`90) they were so stupid to have only one fixed frequency. Thought todays cards support variable (e.g. 11kHz to 96kHz) frequencies.
About the topic:
For classic 8 bit sample stuff you will more or less have small differences in quality (emulation <> original). If you use tracker like DigiboosterPro/OctamedSoundStuio or Sequencer like HD-Rec with 16 bit 44,1kHz Samples on Amiga and play the same on emulation on pc you shouldn`t here differences. Ok, the most know this already.
I wouldn`t call an Amiga is something like an synthesizer. I own a roland MC-303 (groovebox) what I wouldn`t call it a synths too because its is sample based with sound manipulation.