I would advocate following the manual. It directs to lube some engine bolts and not others.
Where it tells you to lube them, it also specifies with what.
I do not like to deviate from manual spec unless I know better, as the torque specs will be different between a lubed fastener and a non lubed. Also some threaded bores have a bottom so excess lube cannot escape out the end and may cause hydraulic lock giving premature torque reading.
On occasion I come across a bolt whose threads have somewhat bonded in place, an impact driver or a few sharp hops of a small hammer will break the grip.