On your first point, there is another mechanism which is if the stain was made by someone exiting the shower from where they were showering. The orientation of the bathmat could have been changed by Amanda if she really did a bathmat shuffle where she replaced it where it should go in her own words. But not the very unlikely rotation point.
On the second, there wouldn't be if they had been cleaned. We know that there isn't any evidence of egregiously stepping in the main areas of blood. Meredith was killed in the far corner of the room, on her knees facing away from the attackers who were restraining her. We know that *no-one* stepped in the very thickest part of the blood stains.
On the reason for the bathmat still being left there, Amanda and Raffaele were reported as being "startled" when the police turned up and they were sat with the mops outside the house, probably trying to get some fresh air and think. They knew they had a number of problems outstanding as they had not yet finished with the clean-up. She knew there was blood on the faucet, in the sink and on the mat which she nevertheless used to do the bathmat shuffle despite the fact that she thought it was menstrual blood (one look at it, makes this very hard to believe, surely, even to people who believe her) and that it was "ewwww". Amanda detailed all of these locations of blood in her extraordinarily micro-detailed alibi creation in her email home to friends and family written in the small hours of the fourth of November.
She knew she had to account for all of it and came up with all of the ideas in that extraordinary 2,900 word email in the early hours of the 4th, 1,900 words of which are taken up by the incredibly fine detail of her movements on the 1st and 2nd *before* the finding of the body. It smacks of someone trying to create a detailed alibi for themselves before they have to go back for questioning. It's an email where there is one reference to Meredith being "beautiful, funny". There are no references in 2,900 words whatsoever about feelings of grief, fright, horror, terrible thoughts about if she suffered, *nothing* that one gets from friends in such situations. She does talk about being "bummed" about having to move out of the house though...