use microphones with tight patterns and arrange everyone in the room appropriately and at decent volume and bleed becomes much less of an issue.
in our one room set up i use overheads with a clean off axis response and a somewhat tight pattern...
mkh40's in an x/y arrangement just over the drummer head. kick i usually have a d112 with a packing blanket over the kick. snare the 57. toms tightly miced with 012's. drum set is in a corner facing out into the middle. we can usually cut out guitars entirely and it sounds clean...
guitar amps are either coles, bk5, 77, or an SM7 (most often) in side corners...amps are pointed into the middle of the room. mics are pointed so the off axis is away from the drums.
bass is about 5 feet from the drums... 421, 4047, and a DI is my standard set up. amp is also pointed in the middle of the room. we use a gobo here in between the bass and the drums.
bleed is rarely an issue once the band gets going and gets comfortable with the sound in the room. if there's a guitar player who insists on being at 10 with a full stack while tracking - well - that sacrifices the sound IMO but it's their choice. in my imperfect world i try to save that type of stuff for reamping or an overdub...but sometimes the band loves the bleed...usually the punk/garagey stuff.
hi hat in guitar amp mics is a rough one. try using packing blankets over the amps if you can. if they're tube- leave room for ventilation!
snare rattle can also be an issue. i listen to 'the wind crys mary' a lot and tell myself it's art.
PS- no headphones are being used usually. sometimes the drummer takes a click in one.
Mike