yes, there is an enormous difference in the bases...Not to hijack the thread but I acquired a couple of Sanwa JJLJ-PL2-8V however @alberto1225 repro panel he specifies it should fit the Sega Saturn sticks. Is there any difference in width or the base that would prevent the Sanwa from fitting?
I've stated it many times before but pretty much every version of the these sticks have different mounting requirements.
That's not to say you can't make it work, but don't expect this stuff to just drop right in. Even codecrank here used adapter plates to make it work.
With the Sanwa JJLJ-PL2-V8 you may have other issues regarding depth as well.