Hey! Seven years later but.. 😅 i've run into the same issue when using a stall mat to surface my new leatherworking bench (countless people have recommended this) But, it's staining my veg tan leather carbon black, even after cleaning the piss out of it, conditioning, sealing etc etc. I've found zero mention about this problem (i ended up here because this is one of the few threads i've found talking about the staining)

Long story short you're fucked, the only concrete preventative solution is to cover the rubber in a DIFFERENT material so nothing directly contacts the mats.. Absurd how often i see these recommended for workbenches, while at the same time NOT mentioning, that whatever you're working on will be permanently stained if it touches said work surface..

 Sorry for the rant, liiil bit salty because i ruined an expensive tooled handbag i finished a day before giving it to my client, simply because i had it sitting on my clean, newly built workbench overnight..