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According to the information published by the HO, EU citizens do not need to submit a passport and the EU ID card is enough. However, I understand that supporting information to prove the 5 years in the UK and ILR is necessary.
Has anyone applied this way, without submitting a passport?

Thanks

You need to have obtained proof of Permanent Residence before you can apply for naturalisation.

Otherwise- no reason why you can't use an EEA ID card. A passport doesn't prove anything since EEA passports are not usually stamped and because the ID card is acceptable for travel, some EEA citizens in the U.K. don't have a passport.

However, you may not find anyone with actual experience of doing this. If the Home Office guidance says it's acceptable- does that matter?

i applied for permanent residency as well as British Citizenship using my French national ID only.
i did not use/mention my French passport at all.
There have been no issues.