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Yes they do take that into account, but if the car was delivered there was no tax paid. FFR only recently started charging tax on picked up kits at the factory. I know, because i picked mine up in june and paid 6.25% tax there.
The only reason why I decided to pick it up was because i found out Pa is a reciprocating state with Massachusetts, so when i register my car, i can show i paid tax already in Mass and they accept that.
That's also why i only got the base kit with minimal options on pick up. It's a lower tax costs.
If i got the complete with $3000 more of options, that would be $1380 tax on a $23000 compete kit build.
Pa dmv only cares about the receipt showing the kit listed. All my other parts bought much later or before need not show proof of tax, nor do they ask.