Actually, it's not because of the gaskets - is because msr fuel bottles are unlined aluminium, and methyl
alcohol can react with aluminium to corrode it and generate hydrogen gas! (See Section 10 in this MSDS , or the warnings about reactivity here..)

The short answer is basically that some alcohols (particularly methyl) can react with alumnium. Storing
fuel in a bottle you intend to have pressurized flamable stuff in that both corrodes it and generates hydrogen gas inside is generally a bad idea. Don't do it kids.. The reaction is slow and won't happen quick, but it'll happen.

Some aluminum fuel bottles (I think the optimus ones) are lined with plastic (like a pop can is), to make it safe to put alcohols in them. MSR ones ain't. Don't put alky in an aluminum fuel bottle unless the bottle maker says it is safe to do so. MSR doesn't say their stove burn alcohol because they know they don't want people putting alky in MSR fuel bottles.