I've done similar things in the past and never got a crash. (even with build .48)
I can confirm that doing similar things as opposed to exactly the same thing won't make OpenMPT crash. Try it without any songs open.
Does it happen with all VSTi plugins?
It happens with all I've tried. (farbrausch V2, tb peach, tb toad, tb monomoachine, tb triforce, cheeze machine)
My songs only use Xlutop Chainer, which could be why I don't have this problem.
I don't think it matters, but I haven't tried it so I wouldn't know.
Does it also happens if there's a VST effect on the chain with normal sample based sounds?
If by that you mean applying an effect to a channel, then no.