The contract would be between LBS and you as the purchaser, so whilst the additional manufacturer’s warranty would be between the purchaser and YT, the actual legal obligations would be being taken on by the shop if they bought it and sold it on to you.
And possibly the manufacturers warranty wouldn’t be applied to you either, as YT could argue that the purchaser was not you etc etc.
Ref VAT, they’d buy the bike inc VAT from YT, sell it to you inc VAT and pay over net the difference between their input VAT and their output VAT (i.e. tax on the “value added”, hence the name!)
So the only way you can get the LBS to make some money off it is to get them to charge you for an initial build or something similar.