It seems that the ico's are embedded in to the layer regardless of rasterizing and such(at least in some cases). Copying the layer then pasting it as a new layer seems to work and prevents the ico plugin from popping up export options.

Probably a good idea to do this for all imported ico's.

Ok, I had some ico's in a folder and it seems if one has any ico in the project that the ico plugin will pop up for export options at some point depending on what is called(in my case, doc.Trim()). It only does this once after project load. My script was ignoring all the ico files I had so I thought it shouldn't matter. Seems to be some kind of initialization issue with the plugin.

Ultimately rasterizing all imported ico's is the solution. Any lingering ico files will trigger the plugin and break the flow.