that link is imho very limited to hole and shaft connection type and i guess used as general rule of thumb for some type of steel.
This is a very standard engineering table.
some are even negative and require heat/cooling process before mating them together.
Yes, those are called interference fits and they are listed in the table.
for example you dont expect a cheap bolt has a perfect X distance between threads, if you do 0.1mm tolerance on the nut
Those tables are for flat mating surfaces. Everything else is derived from those tables. And threads use a completely different system of tolerances.