Once magic gets introduced, things get... Interesting. With a capital I.
I think it would be really neat if you could order an attempt to make a custom hybrid, among other magical projects. Select what traits you want to breed into it, and your wizards will do their best. The more things you specify, rather than leaving to chance, the harder it is and the more failures are likely.
But they may require... breeding stock. And there may be all sorts of unhappy thoughts to being involved in such a project, especially if one of the involved parties is sentient(and doesn't have a specific entry for not minding that perverse sort of thing in the raws). Even if they can be compelled to comply - if that control ever slips...
For natural breeding, though, things would probably be relatively subtle. Breeding only within a "genus", for instance - defining the term loosely, and with, at least, dwarves, elves, and humans probably in the same genus.
Although I still think it would be better to make entries for these hybrids, A) having the support for a "blend" would allow for magic to come and muck with it later, and B) so long as you're not trying anything drastic like differing body structures, there probably is some room to leave it to chance.
Especially if there's going to be in-species variation beyond attribute gains in their current, simplified state.
If any hybrid had, by default, low or nil fertility(i.e. if there's not a viable species listing for it in the raws which would trump the auto-genned figures), that could help keep the hybrids from coming to rule the world - not that it isn't fun to sometimes see other races in a goblin raiding party, for instance, but anyway. For hybrids of sentients, there might be prejudice against them in most races' preferences, making them unlikely to breed and certainly unlikely to become a major portion of the populace. On the other hand, they might also get shoved into military roles, so a fortress might see a disproportionate number of them...