You are perhaps, if I may say so, missing the point of the charge, which is an allegation that City breached the duty to submit its accounts in good faith. Whether a transaction is with a related party is not a black and white issue, its a judgment call. So the League will have to demonstrate that City's judgment call was not made in good faith. As I say I just don't see how you can show that call was made in bad faith when its the same call that was made by the auditors.
As to motivation for the charges, of interest and relevance may be this little snippet from para 185 of the first APT decision
"We accept the evidence of Mr. Herbert and the clubs that gave evidence in these proceedings that both the PL and the clubs had concerns since at least 2018 that the PSR were being circumvented by the failure to report sponsorship agreements with RPTs"
I wonder whether that may provide a suggestion as to where the motivation for the inclusion of this, assuming it to be included at all, within the 115 charges may have originated.