Q: cannot delete mail from storage on iPod

I think you have problem with icloud storage, not on your device.

https://support.apple.com/en-us/HT204247

You can clean out your mail at www.icloud.com by removing all mail from all folders, including trash and "sent".

However 1>

it may be impossible to clean out completely, even if you go and disable icloud mail in settings - icloud - mail and notes by turning both of those off.

2> 5 megabytes are thousand times less then 5 gigabytes that you get from apple and is unlikely the reason of you not being able to backup. While it is possible - very, very improbable.