Maybe they are the same and run on just an internal capcom emulator or maybe they got some changes.
The original-series Mega Man Legacy Collection does use at least an NES emulator (which, given how well Capcom's attempts to recode their games from the ground up have turned out in the past, is probably for the better), so it'd surprise me if the X Legacy Collection didn't.
As far as I know, the only major changes to the games in the X Legacy Collection is changing the Maverick names in X5 to more closely match the original Japanese version (e.g. "Volt Kraken" not "Squid Adler", "Spiral Pegasus" not "The Skiver"). Again, it's probably for the better...as hilariously awful as the name "Duff McWhalen" is.