Lightning is just an off-chain out-branch, which will eventually be re-integrated onto the main blockchain (based on its original funding/terms). The benefit of this is that single entities can branch off the main blockchain, which is limited in its total blocksize/capacity.
The only limits are those by the handling lightning institution. This differs from bitcoin's main public blockchain, which rewards/creates approximately six blocks /hour, each with a limit of just a couple megabytes.
It seems like a major issue when dealing with multimillion dollar transactions.
Let's say I have 1 BTC. I buy something for 1 BTC on lightning network A. Simultaneously (within nanoseconds) I buy something for 1 BTC on lightning network B. I never plan to use BTC again (or if I do, I will use a different wallet, etc.) Do I just get two purchases? Is there a meta-network clearing house, and if so, why are there many disjoint networks.
Or do I need to have moved my BTC into the lightning network A or B before I spend it?
Not on the lightning network. Fees are used to incentivize or disincentivize routes across channels.
> The institution handling this offchaing lightning branch can implement fees in whatever structure you agree to transact, including percentage based.
No institution is needed. Even if one is used as an intermediary, when using lightning non-custodially, the economics of lightning are such that fees are determined by the nodes in the payer's desired route. If it's a custodial transfer from one user to another, no routes are needed.
I imagine the seconds to pay won't be true - if they are exchanging emails and inspecting boats it's going to be an hours to days long process.