I'm applying to a prestigious funding program for early-career researchers* that places a heavy emphasis on the "scientific excellence" and "intellectual capacity and creativity" of the PI. To demonstrate this, the proposal is required to include a section on "early achievements" that lists five top publications, "highlighting those as main author and/or without the co-authorship of [the applicant's] PhD supervisor".
My problem is that my best publications overall, as well as the publications most relevant to my proposal, list my PhD supervisor as the co-author, even though they had no significant involvement, neither in the formulation of the research questions, nor the planning and execution of the experiments, nor the writing up of the research results. This is because I worked in a fairly large research lab where the more experienced doctoral candidates and postdocs were granted considerable autonomy in pursuing their research, but it was the official, documented policy for the lab head to be credited as co-author on all publications, irrespective of their involvement. There was a minor kerfuffle when a colleague of mine pointed out that this policy was at odds with the ethics and authorship guidelines of the journals and proceedings we regularly published in. This resulted in the deletion of the policy from our lab's internal handbook, but the policy continued to be applied in practice.
So I'm wondering what to do about my publication list in the grant application. Should I focus on the publications without my supervisor as the co-author, even though these aren't my strongest or most relevant work? If I do include one or more publications that list my supervisor as co-author, should I explain in the proposal that the co-authorship is purely nominal, or will this come across as suspicious, egotistical, and/or desperate? What course of action is most likely to leave a favorable impression on the reviewers?
*The program is the ERC Starting Grant, though my question is probably relevant for others applying for an ERC Consolidator Grant (which has the same evaluation criteria) or to similar programs from other funding agencies.