After skimming parts of the actual adopted text (its a 537 [albeit wastefully formatted] pdf, dont blame me), which is mostly an update to the old directive, I think I might be able to address some of these concerns. (Not an expert though)

The article never said a company like Apple couldn’t pair the battery to the device and charge €100 for it.

The important part to remember is that this isn't just about consumer rights. Even the first few pages make it very clear that sustainability and battery recycling play a huge goal, ultimately aiming for a "circular economy". While we should for now not debate what that actually means, one part of that is ensuring less waste. Hence the second part of the adopted text, "waste batteries". If companies would simply start making it unfeasible to actually replace a phones batter, we will probably see an update of the directive.

you have to include the plastic casings to ensure that they aren’t damaged when being pulled out or dropped or thrown in bags so you do end up with a thicker device

Fair point, theres probably no objective argument to put against this. My subjective argument would be that the thinness phones have reached is a bit absurd anyways and one or two mm more wont hurt them. I mean, we all put them in cases anyways. If you absolutely need a thinner phone, buy a thinner case.

I also question the viability of it leaving the EU market

Its absolutely not going to happen. Its more likely that we might see a sort of California effect, where manufacturers that have no reason to produce several versions simply start producing only the EU version and market it as sustainable and environmentally conscious in markets where legislation is more lax.

I’m more in favor of right to repair, or basically requiring the parts such as batteries and displays have to be available to everyone

Completely agree. But this wont be the last we see of this, since batteries will continue to be a topic in EU politics. For now, battery collection and recycling are relatively low in the EU, but is supposed to rise in the coming years/decades. To reach that target, more action will be necessary.

Its also important to mention that the adopted text specifically mentions that end-users should be able to replace their batteries without specialised tools, contrasting it later on with "independent professionals" that should replace batteries in unsafe environments:

"A portable battery should be considered to be removable by the end-user when it can be removed with the use of commercially available tools and without requiring the use of specialised tools, unless they are provided free of charge, or proprietary tools, thermal energy or solvents to disassemble it"