There's nothing in the rules that prevents you from having the service of two creatures with the Familiar variant.
What you have to remember is that variant monsters, like monsters, are designed for the GM to use to make enemies more interesting. The Familiar variant is a monster variant, just like the troll's Loathsome Limbs variant or the Genie Powers variant. They're for GM use rather than player use.
The Mage NPC in Appendix B of the Monster Manual also has a Familiar variant, which says:
Any spellcaster that can cast the find familiar spell (such as an archmage or mage) is likely to have a familiar. The familiar can be one of the creatures described in the spell (see the Player’s Handbook) or some other Tiny monster, such as a crawling claw, imp, pseudodragon, or quasit.
So the Familiar variant is for GMs to create more interesting NPCs, rather than to provide players with additional options. Of course, with your GM's permission, you could obtain one of these familiars. This would probably involve actually finding such a creature and somehow forming a bond with it. But this relies solely on your GM to allow and arbitrate.
Needless to say, if even getting one familiar this way is entirely up to your GM, getting two is, even more so. There's nothing in the rules to prevent it, but you'll have to talk your GM into it if you want to have a quasit on each shoulder.
Now for combining Find Familiar with the Familiar variant: The interpretation that causes the least difficulty is that the variant Familiar isn't actually a familiar, it just "serves you as a familiar". In this case, there's no interaction between Find Familiar and the Familiar variant, and everything is fine.
However, if the variant Familiar is a familiar, well...things get weird. If you have your familiar from casting Find Familiar, and you then bond with one from the Familiar variant, there's no way to tell what happens. You "can't have more than one familiar at a time", so you've already put the game in a paradoxical state. Your original familiar might vanish, or your new one might die, or, well, anything, really.
If you have a familiar from the Familiar variant, and you cast Find Familiar, then by the rules (when using the interpretation that variant familiars still count as familiars), you get to change the form of your variant Familiar. You probably don't want to do this, since all the forms you could change it to are weaker than the one you've got, but there it is.
The fact that these rules break down completely when faced with each other is just more evidence - the Monster Manual is not meant as a player resource. Sorry, but it's not. Every spell or ability (like Wild Shape) that would require a player to look at the Monster Manual says "your DM has the stats" or something similar. The Familiar variant was never meant for players to see. It belongs to the GM.
As written it seems the shape of the tumor can be changed each time it is detached from the alchemist's body:
the alchemist can have the tumor detach itself from his body as a separate creature vaguely resembling a kind of animal suitable for a familiar
There is no mention of the first time the tumor is detached being different from the other times, so each time it detaches it gets a shape.
However it seems likely to me that what was meant here was that you had to choose the shape of the tumor the first time it detaches. I think this mostly for a question of balance as making you able to change the tumor's shape at-will makes you able to get +3 to any skill when needed, among other strict benefits compared to a regular familiar.
Best Answer
In 3/3.5e, a familiar is a once-normal animal magically summoned and bonded to a spellcaster by a ritual
This is spelled out pretty clearly in the text describing the familiar class feature (3.5e PHB pg. 52), emphasis mine:
The text here is clear that a familiar was once a normal creature of its type, but it was summoned to service by the ritual performed by a spellcaster, and in doing so gained new magical properties. The two are linked by a magical bond - and indeed losing the familiar causes the master to lose XP, so you could fairly interpret that the familiar has been imbued with some portion of the master's power or essence by this process - but it was definitely originally a normal creature.
This was changed significantly in 5e, where the Find Familiar spell does indeed summon a spirit of some kind in the form of a physical creature.