I like some of these ideas. I don't see companion customization on the level of character customization happening. It'd be cool, but impractical. However, Some customizations that change species could be cool. Now I admit that I hated the idea of companion customizations at first, but the clone issue made me realize that it's necessary. And why is it so bad to have the option of changing a companion's species if we're already changing their race?
I think that the customizations should still be logical though. I haven't gotten past the first chapter for any class besides the Sith Inquisitor, but I'll mention a few ideas about the companions I've encountered. Since I haven't finished many companion story lines, I'm lacking some info that could invalidate some of my observations.
SPOILERS AHEAD
Any companion with a relative that shows up in the game shouldn't have cross-species customizations. Corso's cousin being human when he's a cathar would be weird. Ashara's ancestor is clearly a togruta, so making her human would be odd - not impossible, but a bit hard to believe. And changing the appearance of these NPCs to change based on an equipped customization isn't going to happen.
Companions like Aric Jorgan specifically mention their species in dialogue, so species-altering options for them are out. Yes, they could probably alter that dialogue, but the difficulty of doing so (and figuring out how to do it) make it unlikely to happen. Bioware won't bother.
Obviously companions like Khem Val and T7-N1 that don't show equipped armor can't be changed into humans. If nothing else, that would alter their height, potentially causing issues with dialogue and combat animations. All we can do is hope for customizations that make them look very different, but still leave their species the same.
I think any companions that don't speak basic fall under this category as well. I mean, can you imagine how ridiculous it would be to see a human Bowdaar speaking Shyriiwook?
Now there are still plenty of companions that could have species-changing customizations. To my knowledge, Kira's never explicitly referred to as human. Assuming that's true, she could plausibly be a twi'lek, zabrak, mirialan. cathar, or miraluka. Any other playable species I think would be a bit more unusual in the Jedi Order, and wouldn't make quite as much sense story-wise.
Andronicus Revel could totally be any of the species Kira could be (although miraluka might be a bit odd) and I can see him as a chiss or rattataki as well. Considering his lack of background information, he could even be a non-playable species like togruta or nautolan.
Someone like Malavai Quinn, who has clear ties to the empire, would most likely be an Imperial-aligned species. Maybe chiss or zabrak, but I think he'd make a great sith pureblood. A sniveling, non-force sensitive pureblood trying to justify his existence seems fitting.
There could definitely be some exceptions. I know that Kaliyo specifically came from Rattatak, but she could be a hybrid similar to Aurra Sing. I'd imagine that Bioware would be able to use some cc options from other species for companion customizations. If that's true, they could give Kaliyo some hair (like a Mohawk, nothing to girly) or maybe give a few non-human companions human eye colors, hairstyles, or cybernetic enhancements.
This post got a bit longer than I anticipated, so sorry about that. But the lack of companion customization does suck. As much as I'd love to have fewer human companions, I also love for the non-human ones to get more variety. Honestly, Ashara needs options that don't just make her a clone of other NPCs. I also wouldn't mind some customizations that do or don't include "iconic" features. I wouldn't mind a few new customizations for Quinn that include his mole, but I'd also really love a look for Doc that doesn't include a mustache. I'm sorry but I can't stand beardless mustaches on my men.
And for non-playable species, let's at least make them a bit different than the NPCs. For example, if a female companion was going to be given a nautolan customization, I'd like it to be someone with body type 2. I've only seen female nautolans with body type 1. Same goes for togruta (of both genders) all being body type 2.
Long story short, please give use more variety!