Should a US-based writer avoid a UK-based indie publisher?... or does it matter?
A lot of it depends on the size of said UK indie publisher. Being indie doesn't necessarily mean small, especially if your definition of indie just means "Not Big Five."
Like, in the adult science fiction/fantasy area, the UK's actually got two pretty big indie publishers in Angry Robot and Rebellion. Both of them have put out award winning books over the last several years, and accept submissions either through the occasional open call, but mostly through agented submissions, and they have global reach. When you publish with them for World English rights, your books will appear in North American bookstores, not just UK ones.
A lot of this also depends on what kind of deal you wrangle with such a publisher, and which rights they hold onto versus what you retain. I'm Canadian, but my agent got me a book deal with Rebellion. She did all the usual due diligence negotiating advances, royalties, etc, but because of Rebellion's reach, the book will be distributed in North America through Big Five partners. In Canada, for instance, Rebellion will distribute my book through Simon & Schuster Canada, so both big chains and mom n' pop/indie bookstores can still stock it they decide to.
If you're worried about the legal stuff, you're best off asking a professional, like an agent. If you have potential deal in hand, you might have some luck asking an agent to represent that deal to make sure your writer rights are protected. Otherwise, it's just like entering into any contract; read it carefully, and if there are things you don't understand that you're worried about, get someone with legal/contractual experience to look at it.