Intolerance of dogwhistling is what people refer to when they say that intolerance of intolerance is bad. The problem is that when you start judging people based on what you think are dogwhistling instead of their stated opinions you start getting very close to creating an oppressive regime.

Example problems: Many racists use anti-immigrant rhetoric, so an anti-racist might take all anti-immigrant rhetoric to be dogwhistling for racism. Many man haters use feminist rhetoric, so an MRA might take all feminist rhetoric to be dogwhistling for man haters.

Both sides then starts seeing the other side as rabid haters sending subtle signals of hate all over the place. As a result both sides gets attacked for having valid opinions and can thus justly declare the other side irrational. Do you see how that can easily make things escalate out of control?

Do you think such escalations leads to more tolerance? I don't. The only way to get a tolerant society is to accept a bit of intolerance, similar to how we have to accept that there are sometimes insect parts in flour, while those insect parts are bad the measures we would need to implement to get them out would force us to throw away tons of perfectly fine goods.