I don't think it's something that has been asked before, the Manifest editor does have a RemovePermission command. That may do what you want, although I don't think that B4a adds additional permissions that are not related to a library that says it needs them.
The only thing I can think of is perhaps using a webview for internally generated html, you might consider removing the internet permission. Whether that would actually still allow use of the WebView I don't know, I haven't tried it.
Out of interest, what permissions are you looking to remove?