Because they are always things people forget and almost always have to be done.
A stocko 25 turbo will choke a 3L as well.
I did an engine swap myself (rb25 neo) and it has cost ~$3500 so far and I already had clutch, tyres, fuel pump, injectors, turbo, intercooler, piping etc. And I did all the work myself, old engine out, new engine in. The motor was $1900 bare and the rest was for tuning and buying new gaskets, bolts, random parts, getting broken studs removed etc etc.