Could HubSpot potentially filter data by email client? I feel like that would be our best bet initially to help filter out some of the false positives. For example, look at email open rates for Apple Mail pre and post update and compare them. Also, if a user becomes engaged for the first time in a long time, but uses Apple Mail, maybe designate that somehow. Just some of my thoughts!
In addition to filters like "Email open was last using Apple Mail", or "Contact has ever opened with Apple Mail" etc., Hubspot could also work in the way the way Refine by Date is included in some filters.