A long, long time ago (probably only in the first few years of the project) there was a text file with MAME where some of these differences were noted, but as a whole it can be very difficult to see / notice revision differences without pulling apart the game code and finding exactly what was changed (which is very time consuming) Some MAME source files still document this a little, but it's not something we ever need to know as part of reverse engineering the hardware, so it's more fitting for a community project to document what is changed.
A lot of the time differences are simple bugfixes for cases you might never encounter, but players encountered enough during real use that it was felt necessary for a fix to be issued. For example, with Joe and Mac Returns the difference between the revisions is just a bit of code that checks when you're entering a bonus stage as in the earlier revision it's possible to softlock the game by entering a bonus stage at the same time as other things occur.
With things like fighting games you often saw things being rebalanced over time if one character was found to be overpowered, or you could win without the other player having a chance, regardless of skill (infinite combos and the like)
Other differences are less interesting, maybe a game was rebuilt just to add an extra copyright string, thus shifting a large amount of code and data for no significant change at all.
US revisions are actually usually much less fair, and designed to eat your money with nasty difficulty spikes, poor game balance etc. Raiden is a bit of an exception there in that the US version becomes easier with the ditching of checkpoints (although there is logic behind it, American operators wanted people to coinfeed through games as finishing them gives people a false sense that they're good at them and more likely to want to show off, whereas sending you back to a checkpoint requires a player to have skill and means they're less likely to coinfeed and more likely to ragequit)
On the subject of Seibu / Raiden, there are actually many code revisions for things like Raiden Fighters (beyond the sets that differ only in region byte) and likewise plenty of actual code revisions on Raiden 2 (even if the vast majority of sets are based on the same code revision) The MAME source actually groups the Raiden 2 sets based on code revision, even if gameplay differences aren't obvious beyond between the 'easy' 'normal' and 'harder' designations..
With Raiden DX the Japan version lacks autofire on button C, the theory there is that while in Japan you could easily get cabs with autofire hacked onto the control panel as a mechanical function, outside of Japan that never happened so it was mapped to a game function instead.
But yes, MAME supports many thousands of clones, some more interesting than others, don't let anybody ever tell you that only the parent sets are interesting, or that clones are a was of time / space / effort dumping because in many cases it's simply not true.
Documenting the exact differences is a project in it's own right tho.