Since it is not a mod or other external software altering the game externally, but since it still allows you to edit the world generation precisely as you'd like, giving an advantage on people using base world gen, and especially since world gen is no longer part of the run, is it allowed to use advanced world generation for speedruns?

No, as the rules say, only changing between the default non-advanced settings are allowed.

The worry is that, if custom seeds and advanced tinkering is allowed, runs would devolve into all being in the same best world people have found. It's much more interesting for many to devise general strategies, rather than do the same run over and over in identical circumstances.