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So I want to preface this post by saying I'm a total amateur when it comes to hacking and don't have deep knowledge about anything Gen 2 besides things related to music hacking. I may be interpreting this stuff wrong, and just want to get that out of the way in case I spread misinformation.
I'm doing some research into Varaneous (and by research I mean fucking around with the roaming map coordinates in trial-and-error) and it looks like, at least for me, it starts itself in a map that doesn't exist.
GSC separates maps by groups. You can have 255 mapgroups, and 255 maps in each group (or so I think; I haven't messed with this shit too much, it might be less, but it has a full byte stored for each at least). Prism uses 95 different mapgroups. For me (and I assume for others because the Pokédex showed Varaneous in the same place as everyone else, seemingly on Route 68), Varaneous seemed to be on the 255th mapgroup, in the 167th map of that group. Obviously that doesn't exist as a map, and it doesn't have any routing with other maps for Varaneous to go to either, though that specific combination of mapgroup and map number does display it as being in the same place as Route 68.
When I moved it to a map that actually does exist, i.e. moving it to Route 70, mapgroup 14/map number 1, it displays normal roaming Legendary behavior. I think if someone added a script to give it a default starting map like that, Varaneous would no longer be bugged.
This also means the people claiming to have found him on Route 68 either didn't have this problem for some reason or they're full of shit.