When adding a .m or .mm file with the Projucer is there anyway to specific you want ARC enabled for that file? -fobjc-arc?

We don’t store any file-specific flags at all… Is it even possible to safely link together object files that are compiled with and without ARC?

As far as I know, yes, this is possible.
In Xcode, in the Project settings/Build Phases tab there’s a “Compile Sources” section where you can add specific Compiler Flags for each file.
So, for instance, you can add -fno-objc-arc if you want to compile a non-ARC file within a project that uses ARC and -fobjc-arc if you want to do the opposite.
In order to avoid misuses, I usually add this at the beginning of a file (.m or .mm) that I know is going to be added to new projects where ARC is not enabled:

#if ! __has_feature(objc_arc)
#error This file must be compiled with ARC. Either turn on ARC for the project or use -fobjc-arc flag

This said, it would be great if JUCE’s native bindings for iOS and macOS could finally migrate to ARC (it’s 2018…).

Yes, as masshacker says, no issues combining arc and non-arc code.