THere are many reasons why the same digital recording in multiple formats could sound different.
Beyond the usual hardware related reasons why any two sources might sound different, with digital throw any possible number of software related factors/differences that could come into play in any case comparing any two.
It's way harder to identify cause and effect with computer audio for certain compared to anything before it.
Luckily, when done well, the differences will often be subtle and not significant for many, but I feel sorry for anyone predisposed to account for any difference in sound perceived when they hear it, because it is pretty much an impossible chase.
It's easy for me to understand why traditional audiophiles often despise computer audio. There are so many more variables and unknowns to deal with. And so many ways to draw fast conclusions that might not turn out to be accurate. Can definitely drive a control freak crazy.