is it safe to plug an iphone into your pc and upload files or will apple package it with its software somehow

As long as you say the same for Google and Microsoft, I agree.
- Technically android is open source, though. You could install AOSP on a device and not use any Google services
- Microsoft has been contributing a ton to FOSS the last 5 or 6 years.
  Their flagship programming language, .net, is fully OSS and runs best on Linux.

What are you trying to do here?

just transfer files
- see this article:
  https://www.tomsguide.com/how-to/how-to-transfer-photos-from-iphone-to-computer

There is no problem connecting an iPhone to a PC. Generally, Apple requires iTunes to interact with the device, as they wish to restrict and monitor the way you interact with the device. There used to be a FOSS plugin that worked with Apple on Linux, but it was not stable when I was fighting with it back on the iPhone 5.

You don’t even need to do that. You can side-load iOS compatible apps through the web browser. The device needs to either be in developer mode or provisioned with a configuration profile for the app (or app signing key) in question, iirc.

It’s quite a pointless effort, though - using an open source licence and having the source code publicly available is the best you should really try to get for iOS apps. But I’m guessing this is just a theoretical thought experiment.

I don't think anyone can really say, but I'm not an expert on security.

My biggest skepticism is that all phones have untrusted proprietary hardware. Apple does its own thing and usually seems to develop stuff like a full stack. However, I don't think there has ever been a documented cellular modem. I don't trust anything on a PC unless it is running libre boot. Like even UEFI has network access. You likely also have an entire Intel ME operating system or the AMD equivalent running with lower level permissions than root at all times. Maybe if you have an extensive SELinux ruleset you could mitigate any potential.

If your software is signed or has a hash key available, you can use that to verify file status.

I haven't had any issues with AOSP and GrapheneOS, but I go as far as installing a fresh OS on an old laptop, setup a custom network, all just to install chrome and do the easy automated ROM swap to run GrapheneOS. Then I format the drive. It is the only way I care to run regular chrome or connect Google tainted hardware.

You can install Graphene without Chrome, just so you know - might be worth looking into, since it sounds like you’re taking this stuff seriously - good for you. But yeah, at a certain point, can you trust the Graphene hashes haven’t been altered? You can take it to extremes.
- We all have our thresholds. I use this mostly to learn using the practical application of an example. I do care about my actual workstation and what is on it, mostly for the peace of mind, but also because I might occasionally get pissed off at some piece of shit proprietary hardware, reverse engineer the design with a schematic and upload it with kicad files. That's about the only real reason for me. I also source a lot of sketchy datasheets and old documentation. I care enough to be behind a whitelist fw, which would stop most junk. It's mostly just the principal of ownership. Stalkerware is hacking as privateers with a license from the king of the USA - corporate America.

I believe the iPhone uses a basic read-only protocol to access media. (MTP?) You can use iTunes to add files to the iPhone but that's not FOSS. I personally use Photosync, you might like that for wireless photo transfers.