Yesterday I moved from https://www.domain1.com to https://www.domain2.com/test and had the only issue with network path I described above.
What you describe sounds a bit more weird: you want to move from a sub-domain to the same main domain or to the main domain’s sub-folder that has the same name as the sub-domain?
Yes, that sounds a bit twisted and I wouldn’t go that way – directly.
I don’t know what the authors of the plugin would recommend, but I would rather do this in 2 steps: first move to a whatever test domain elsewhere and then re-move from there to your new address.
But if your final destination is a sub-folder, you’ll encounter the same issue as myself yesterday: everything works absolutely fine, except that when you click on top menu My Sites-Network Admin you get the domain’s root address and not the sub-folders one (but you just edit the address in the browser and it works). I’m sure this can be fixed somewhere – maybe in config.php? – but I didn’t investigate further as this is OK for me as it is just a testing network and my original installation is the initial one.