I much prefer crawl's auto-pickup system (which is automatically disabled if there's an enemy in sight, though it is kind of annoying having to drop things I've id'ed as useless/worse already while using auto-explore).
The autopickup disabling's definable, and only for DCSS, AFAIR.
And you know, you can always disable autopickup (ctrl-a) before exploring ;) I think there's also a place on the configuration file to add *specific* items you want removed from the autopickup (initially disabled, containing ?ofRU).
Stone Soup's autopickup's set for jewelry and consumables (?, !, /, %). Linley's is set for the same minus %, which I find better, as I hate gathering the dead. Modding this to DoomRL, I'd say | and + are on the list.
However, DC's, compared with DoomRL, a very long game with dangers far between. There's little point in having autoactions in a game where every move counts (I don't use the DoomRL run commands for this reason), whereas in DC, not having them could create a manual pickup/move pattern that would likely get me killed sooner or later (ctrl-a when monster's are afoot's hardly mind-numbing, and I've recently discovered that running's often safer for me than manual one-by-ones (as I find specific placement to be less crucial in DC than in DoomRL, though a wasted turn walking in a bad direction due to bad reactions' a killer)).