Apropos the clothing, it's already been noted that Kelly took in laundry and the occasional female lodger, so it's quite possible that some of the clothing did not belong to Kelly.
We also know Sam that Maria claimed that some of the garments found were her laundry, presumably laundry that she did for others to make a few coins. In that context, I think Mary's proximity to fresh water, the ability to heat that water, and to wash several garments at once in a tub, might have lured Maria there in the first place that day. It was said that they spent the afternoon in that room. We also know that she gave Mary a few coins that night.
In some ways I am more interested in the burnt clothing than the others. I find it puzzling that after sieving ashes Friday afternoon and recovering items from the ashes, Abberline and a few of his squad returned to the room to sieve again Saturday morning. I, like Abberline, think that there may have been some interesting clues in the soot.
I agree with your last statement and yes I think it was an intruder.
In terms of defensive wounds-I think it shows, if anything, that she was not already completely incapacitated when he started to cut her throat-ie. strangled to death or unconsciousness. It may point to an intruder who snuck in while she was passed out and attacked her without strangling first or it could have been someone who she invited in-Blotchy who waited till she passed out and did the same.
Don't see how defensive wounds exclusively points to an intruder.
A client before or after Blotchy is less likely because how did the killer knew that Kelly was with somebody or not,making the killing undoable because of the noise/commotion.He would have to stand/listen outside the room,"put their hand through the broken window, and moved back the catch" [Abberline],how did he knew Kelly was asleep,half-asleep.
Blotchy on the other knew Kelly was drunk,alone,asleep and possibly left the door unlocked in the first place and returned.