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Not damned by not having a research letter. Your involvement in the research projects will be relatively obvious from your authorships and your essays.

I would encourage you to make an appointment with the PI and see what his reaction is. Worst case scenario he either ignores you, or you get the sense that his letter will be trash due to his disinterest. If it's the latter, you can simply choose to not submit his letter.
 
Letters are there to show your character and work effort. If your PI can't comment on that, don't get one. If there is another researcher, lab coordinator, etc that knows you better, ask them. That is not a red flag. Admins have done this enough to know that some PIs and MDs are dinguses or just write a generic form letter. Focus on having strong professor letters.
 
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