In the ‘options’ dialog, below ‘integration’ (at the bottom) add as simple ‘associate’ sections
where the user can set an alternative application for an extension.
It does not have to be extensive, just simple, for example user clicks ‘+’ 2 inputfields appear below
…
extension: txt
application: d:\portableapps\notepad++\notepad++.exe
…
Maybe even add the option to add mutliple applications, this would mean a small popup would appear and then let the user choose the preferrede application.
Example, user has set windows notepad and notepad++ for ‘txt’ files. When an textfile is opened a small popup appears asking which application (notepad or notepad++) to open the textfile with.