I'm experiencing the same issue. It's a bit disheartening, I upgraded to Ultimate solely because of Lense-enhanced assistants.
In my case, the assistant did seem to respect Lenses for some queries, but not for others. It also seemed sometimes to completely ignore all proprompting or instructions, as if the query were processed by the base un-instructed model. In some cases it would just switch to other models; This happened often when regenerating responses, it'll stop using the custom assistant's designated model, and find its way to Claude.
*Edit: For reference, I have a lense set to only *.msdmanuals.com/professional, *.merckmanuals.com/professional, *.fpnotebook.com
(Thought it might be an issue that I included /professional initially, but it made no difference)
Quite unusable for me in its current state.