For anyone that cares to know the answer: yes, it is possible. I have three instances running. Matt from support was very helpful and sent me the solution:
Running multiple instances of a plugin isn’t supported by built-in functionality, but you can hack it by duplicating the plugin and editing the Info.plist file inside the plugin bundle Contents folder:
<key>CFBundleDisplayName</key>
<string>Rename this to something unique for Indigo’s UI</string>
<key>CFBundleIdentifier</key>
<string>Add a numerical 2 to the end of whatever is here so it is unique</string>
Since this isn’t an officially supported feature, I’d suggest trying it out in the trial version of Indigo to make sure it works for you.