Here's a possible rebuttal.
1) Nothing in S&S is conclusive in this regard. Which graveyard are they looking at "there below" from the Conservatory? It isn't clear. It could just as easily be the family plot towards the front as the other cemetery out back. Later: "Our adventurous pair descended the steps to the ground level and began their walk through the private burial grounds trying to find their way out of this living nightmare. They passed an old caretaker holding a lantern, too frightened to speak." Well, we know the caretaker is situated at the cemetery entrance, and they pass him and go in, so apparently they walked through the family plot and then went past the caretaker into the other cemetery.
2) Marc clung stubbornly to the "famous villains" idea, which went back to Ken Anderson. No one else thought it was such a great idea, however, since practically all vestiges of this approach were purged from the final HM, and Marc wasn't able to drag it back in for Tokyo. If Marc lost the argument, then he lost the argument. Someone was saying "no" to it, and winning the argument.
3) The names of the busts are what they're called. No one's name is actually "Cousin Algernon," and no such familial inscriptions are found anywhere in the back, only in the front.
4) Besides the iron gate and sign thing (as GG points out), the headstones in the back cemetery are uniformly older by a century or two (or three) than the front yard ones, suggesting two separate graveyards. Also, the backyard ones are in terrible disrepair, while the front ones look sharp.
5) The English examples of Egyptian-style tombs are in public cemeteries. All we need do is postulate that an eccentric Victorian who bought a mummy (complete with sarcophagus) wanted it eventually buried in his own crypt complex (for that extra touch of authenticity?). Nothing says that guy was a mansion resident. He's just a local guy caught up in Victorian Egypto-mania, and he's reserved some burial space in the public boneyard not only for himself but for his Egyptian souvenirs. Wouldn't surprise me in the least to discover that some nutty Victorians actually did such things.
6) Bluebeard—I hate that thing. It's problematic no matter what you do with it. Best bet? I suppose that the BB descendant with the best claim to seniority wanted to take the family remains with him to America, where he re-interred them. This forces you to take a literary character as a historical character, but since the BB story is based on a real person, you just say that this must be that real person.
7) If these really are tombs of kings and queens and dutchesses and knights, collected from all over the world, they're pretty small and mangy, don't you think?
That leaves only the floutist. Yeah, I'll grant that your first thought would be that he's sitting up in his own grave, but that's not a necessary conclusion. Maybe it's the comfiest spot to sit in, there in the area where the band has decided to set up and play. Reminds him of home. Kinda shy guy, maybe. Is that special pleading? No, because there is a good reason to grant the exception to the rule (i.e. that a ghost may be supposed to be sitting in his own tomb), and that reason is the evidence of the iron gate and the (in the artwork) cemetery sign, which tells us this is a local, public cemetery. Against that stubborn, tangible evidence, we may grant that "Apparently, this time the ghost is not sitting in his own tomb, since he's medieval and this cemetery is not."
EDIT: a few more points in response to Smelly's subsequent post. Doesn't matter if it really is "Whispering Glade" or is a tribute to Forest Lawn, which is not a public cemetery per se. As opposed to a private family plot alongside a private residence, Forest Lawn or "Whispering Glade" (or whatever it is) would be a public cemetery by comparison. And the fact that the knight, executioner, etc. are standing around among recently vacated tombs is hardly proof that those were their tombs. In that scene, tombs are emptying at a horrendous rate everywhere you look.