Before anything else, you need to define your threat model. Decide what you realistically need versus what you just want. Regardless of your choice, always ensure you have an exit strategy.
Specifically, get a custom domain so you own your email address, and back up your 2FA and recovery codes using the 3-2-1 method.
Regarding ecosystems, they aren’t inherently bad unless you’re trapped. Just avoid single points of failure, like storing 2FA codes in your password manager. Scenario such as that, is were putting all your eggs in the same basket can be a negative.
Apple is tricky because their hardware creates a much harder lock in than other providers software.
Don’t make yourself miserable by switching everything at once. Some privacy tools just aren’t as polished as Apple’s yet. Personally, I use the Proton suite for Mail and Pass, and VPN, but I stick with iCloud (with Advanced Data Protection) for files on demand because Proton Drive isn’t really all that great except for just backing up stuff. And I still use Apple notes because I just like it.
When it comes to proton mail going to spam. It is true that their own domains have issues at times. But the solution is a custom domain as I mentioned earlier. Once you set up the proper records (DKIM/SPF), the deliverability issue will vanish. Plus, if you ever want to leave Proton, you just take your domain to the next provider.
Ecosystems are fine if they work for you, provided you hold the keys to leave. Sometimes I ask myself, am I using too many proton services? But then I realized, they work for me, I’m happy with them, and if I actually need to leave them at a moment’s notice, it won’t be a problem for me.
I will always have to have at least a Mac mini for my work, but I also use a Linux as my primary machine. It is possible to walk between worlds and spread things around a little bit while using Apple services, but also diversifying quite a bit.
That’s just what works for me personally, your use case and threat model might be different, but no matter what you do, always ensure you back up your data to at least something. Because so many people don’t do that it seems.