How much assembly is required when an LBS orders a bike? I'm looking to order a Marin Lombard Elite from my LBS but I want to replace the FSA BB and crankset with Shimano or SRAM parts, and change to a 52/36.

When my LBS orders it, does all of that come assembled from the manufacturer usually?  If the former, I'll just take it home and swap everything out myself, but if the latter, then I could bring them the parts when I place the order and they could just swap them in when they build it.
This is determined by your LBS, the relationship you have with them and the bike your buying.

Generally bikes come in flat pack boxes and, with the exception of top end bikes, are partially assembled out of the factory. The reseller needs to attach the handle bar and do a safety check. If you want to change parts out you'll have to pay workshop rates.

However if you a buying a good bike from a good LBS you'll find they'll disassemble the bike, chase and face the head tube, bottom bracket and disc tabs as part of the sale. They'll also make any upgrades that you've asked for, either purchased from them or from a different reseller.

If you're purchasing the parts from them on a new bike you should expect a discounted workshop rate. If your bring the parts you shop be expecting to pay premium workshop rates.

There's no set rule of thumb. However as always ensure you have a good relationship with your LBS and they'll look after you and your bike.