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.