What happens if you use the Optional Class Feature ‘Wild Companion’ when you already have a Familiar already summoned from the spell

It's just a temporary inconvenience, except in a singular case.

Basically, all that a familiar's death means is that you'll have to recast Find Familiar at your earliest convenience (so it means the loss of a spell slot for a day if you have a time pressure and can't take the extra 10 minutes to cast it as a ritual). The spell/ritual does cost 10gp, but that's a pretty trivial amount for an adventurer. It also has a casting time of 1 hr so your party probably needs a short rest while you do it rather than simply doing it between encounters.

The only case where having a familiar come to harm is a permanent issue is in the rare event that you decided to retrain the spell (or as a wizard, have lost the spell book that contains it). These are the only times when losing a familiar has long term ramifications.

As to whether or not the newfound familiar obtained when you recast the spell is the same being reincarnated/resurrected, or a different being entirely, this is up to you and the flavor you choose for your familiar.

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.