From my time playing around in the IP&S universe, I understood "poofdom" as being the result of a fictional character realising that she or he is fictional. The character "poofs" and the universe reloads as if the character never existed. You may want to ask Steff for the exact logic as I'm going just by memory here.
So, just Michael J. Nelson and Crow meeting wouldn't be enough to cause this form of poofdom, unless Michael addressed the fact that Crow is just a puppet in a studio.
However, because MST3K is a show that twists the line between reality and fiction, I think the two Mikes could co-exist. Prisoners of Gravity had a similar take on reality/fiction and a interesting example for this idea (characters and actors co-existing) from that canon can be heard here. Of note is Commander Rick's comment "And something called Four on the Floor". Four on the Floor was a Canadian comedy series from the mid-80s that starred a group called The Frantics. Rick Green was a member this group and he later went on to co-create Prisoners of Gravity and play Commander Rick in that series.
So... Commander Rick and Rick Green are both able to co-exist in this universe and, at the very least, Commander Rick is aware of Rick Green's existence. For some reason, poofdom doesn't occur. Therefore, we can guess that the two Mikes can be aware of each other and co-exist without poofdom setting in.
I think too much.
So, just Michael J. Nelson and Crow meeting wouldn't be enough to cause this form of poofdom, unless Michael addressed the fact that Crow is just a puppet in a studio.
However, because MST3K is a show that twists the line between reality and fiction, I think the two Mikes could co-exist. Prisoners of Gravity had a similar take on reality/fiction and a interesting example for this idea (characters and actors co-existing) from that canon can be heard here. Of note is Commander Rick's comment "And something called Four on the Floor". Four on the Floor was a Canadian comedy series from the mid-80s that starred a group called The Frantics. Rick Green was a member this group and he later went on to co-create Prisoners of Gravity and play Commander Rick in that series.
So... Commander Rick and Rick Green are both able to co-exist in this universe and, at the very least, Commander Rick is aware of Rick Green's existence. For some reason, poofdom doesn't occur. Therefore, we can guess that the two Mikes can be aware of each other and co-exist without poofdom setting in.
I hope that makes sense.