This is where I believe you are making a false connection - from what I understand about how safari extensions work, certain permissions are an all or nothing type of choice. So if you want your blocker to inject JavaScript and/or modify CSS, the extension needs full access.
The question remains, whether Adguard do this for some nefarious purpose (your claim), or if they are simply trying to work around the limitations of safari content blocking (which is quite well established can't block as much as JavaScript based adblockers) as they claim.
Given the evidence provided by both sides, I choose to believe the truth is closer to what Adguard claim.