You can sync photos with tools like Syncthing, but it's not automatic because of how iOS stores photos.

You kind of are forced to use it app store aside.

In the EU at least, that restriction will be gone in a couple months.

You can not use iMessage without an apple ID but you could use RCS without a Google account.

You can use SMS without an Apple ID, and iMessage falls back gracefully to SMS. Photos will be lower quality and sending messages to international phone numbers will be expensive... but it will work and RCS support is coming to iPhone later this year which should fix both of those.

Another bigger drawback to not using an Apple ID is backing up is going to be an absolute pain.

Not really. You just plug it into a PC with a USB cable, and it automatically does a backup. You could just do that every night to charge your phone.

Because you can’t access the file system on iOS, for things like photos and contacts or messages, your only options would be iCloud as far as I know (I could be wrong) or I guess if you have a Macbook as well Airdrop?

Yeah you're wrong. The "Files" app on iOS, which is also embedded in various apps as a file open/save/import/export/share/etc option, has a plugin architecture where third party apps can provide all the same file storage as iCloud. You can use Google Drive, Microsoft OneDrive, Dropbox, Bit Torrent Sync, an Git server, etc, etc by simply installing a third party apps.

In fact, Apple charges monthly fee to use iCloud in the files app (assuming you want to store a reasonable amount of data in the cloud). As far as I know, most iPhone users don't pay and a lot of those people would be using third party file apps.

Access to photos/contacts/calendar/etc is also fully available via an API, though I'd encourage you not to let apps access that data. There's quite a long history of it being used for some really creepy levels of tracking — for example, most photos have metadata including date/time/location and face recognition is trivial these days. You're handing over a detailed location history for both yourself and anyone you've ever photographed by giving access to your data, and third party apps have been caught using this for malicious purposes. Sometimes unwittingly, as part of a third party library. Obviously it depends on the app - if you want Flickr to be your cloud storage/backup for your photo library, that's probably safe (and Flickr does have that feature).

Connecting an iPhone to an Apple ID is entirely optional. The only requirement is a quick check on first run wether or not the device has been reported as stolen. The App Store is the only essential functionality that requires an account with Apple even that is technically optional (you can sideload enterprise/school/work related apps for example as well as if you're a developer you can sideload your own apps, and you can do all of that without an Apple ID on the device (the developer/enterprise/school/etc will need an account).