Some random thoughts:
Remember with the Bridge you have choices of where various decodings happen: you can choose to decode in the computer and send linear PCM or to send files in their original format and have the Bridge do the decoding so if a Bridge is involved in these comparisons then it matters where the decoding is being done (for each format): you may be comparing apples to oranges if you are assuming all differences come from different formats.
In general I usually blame the computer (or the sensitivity of the interface card) for things sounding different in different source formats. It may be more productive to concentrate there, e.g. which outlet things are plugged into, (as people have mentioned above) the quality of the cable’s shielding or grounding, etc.
Electrical isolation is a good idea, but not all isolators are created equal: most of the chips available for isolation are designed for use in industrial settings or isolated power supplies, etc. i.e. they assume they are in a noisy digital environment and that are mostly designed for surviving higher voltage differences (e.g. 1000VAC) not for minimizing electrical noise (conducted or radiated.) Further, most are designed for passing high frequencies (they turn high frequency signals on and off to send 1s and 0s) so they won’t really filter out those high frequencies in the digital connection and will add high frequency interference to the connection. If the full isolation unit is built in a single box and doesn’t have a shield between the input and output electronics it also can easily pass non-conducted (RFI, etc) interference between the input and outputs…
Some isolation units can also transmit power from one side to the other and it’s tempting to use them - but they pass high frequency signals with huge current spikes, which, in essence means they are little radio transmitters - they often have ap notes for the chip user on how to pass FCC with their chips so they clearly are generating signals that aren’t good for audio systems. I’d be skeptical of an isolation unit that didn’t have a separate power supply (powered from outside the isolation unit) for each side of the isolator (USB can provide power for the computer side of the interface, but you’d still need a quality power supply for the DAC side.)
Also FWIW until recently USB isolator chips didn’t support USB 2.0 (“high speed”) so they didn’t handle anything above 96k and weren’t good for audio.
My point in all of this is that there’s a lot more going on than you might think between the computer and the DAC and it’s not a surprise that with many systems which programs the computer is running affect the output of the audio system (with many possible interference paths between the computer and the rest of the audio system not even involving the DAC.) When someone says that they have a great computer setup for audio I listen while doing a CD rip at the same time on the source computer and if ripping changes the audio output of the sound system I pass on the computer setup.