I'm in the UK so I would like to have a keyboard that has the at-symbol and inverted-commas in the correct places for my fingers. The Keychron Qn Pros all come with keycaps that have the ats and inverted-commas the "wrong way round" for me so I was wondering if I buy a Q2 Pro and a set of keycaps, will I be able to put on the keycaps that I want and remap the two keys using Via so that they send the correct characters?
Yes you should be fine if you do that. Just make sure your switches are compatible with your keycaps (very unlikely the aren't compatible) and you'll be golden.
The layout is defined by what you set on your computer, it doesn't have to match what's on the keycaps. The only thing to look out for is ANSI vs ISO, UK keyboards have an extra key instead of a longer shift key so you'll want an ISO variant of the keyboard.
If you want some keycaps with UK legends, make sure they include a 1.75u right shift if your keyboard has that. Other than that, the keychrons have standard layouts.