Totally.

I guess the privacy advantage of a regular SIM is that as soon as you pop out the sim card out of your phone, towers can't track you anymore.

With eSIMs on the other hand, I can never truly trust that an eSIM is de-activated? Feels like you actually just have a permanent sim card in your phone and your phone can just be tracked no matter the status of your eSIM. Or is this not technically possible?

I can't give you an answer, but what I can tell is that, unfortunately, being on iOS, you won't have a lot of options when it comes to FOSS apps.

Apple charges developers $100/year to be able to publish on the app store, so that gives very little incentives for iOS developers to publish their app without any kind of monetization, whether via a subscription, ads, or mass data gathering.

I have a lot of respect for FOSS apps on iOS, because not only do devs offer an app FOSS, but they're paying that $100/year out of their own pocket.