There are three issues here in terms of billing and expense:
The setup time for the laptop itself:
- If you're billing by the hour and they've sent you equipment that needed to be set up to allow you to work in their environment (installing software, registering phones, creating emails and accounts, etc), you absolutely should be billing them for the hour/s you took to set it up. It was a request that they made on your time.
The cost of the extra equipment that you ordered:
- Before buying anything, it's always worth asking the employer whether they already have any of the stuff you need sitting in store cupboards at their office or whether they're happy to expense them back to you. If you ask for basic bits like docking stations and cables the company might be happy to order them, noting that employers, even freelance employers, often have a minimum obligation to provide equipment that is ergonomically appropriate for their workers.
The setup time for things you've bought independently:
- This one is on you. If you bought a desk to allow you to work more comfortably with a perfectly good laptop, you wouldn't expect the company to pay you to put it together. The same goes for customising your equipment with non-standard bling like wireless keyboards and KVM switches to allow you to control your laptop remotely. That's not their issue, it's yours.
That all being said, the easiest way to work out a billing issue is, obviously, to ask your employer. If they say that they're happy, bill them. If they say that they aren't, then don't.