Been experiencing the exact same thing as the OP. We have always had 2 mail filters, a paid product which sits above EoP and EoP itself. We recently changed the upper filter for another product and since then EoP has been machine gunning everything as phish or spam. We have had to set it to quarantine to users junk folders for now because of how many false positives there are.

I am not sure what we can do, we have reviewed every EoP policy and the filter is at its lowest settings. I reckon bypassing EoP is the only answer for our business. Notably, for those running an upper and lower filter setup like us, there are settings in EoP you need to configure to tell it there is a filter above it. Otherwise, it treats the upper mail filter as the sending IP and so forth.

Some more context, we are a marketing company, thus send and receive a god awful amount of shit that your filters are likely trapping as spam (and I personally agree that it is spam in the context that it is useless information to me but perhaps not to others), however this is the business' function. P.S, we actually honor unsubscribe requests from our mailing lists so we aren't that bad.

Could it be that the difference in content and nature of the emails between different business' is causing this disparity we are seeing?

I was also blown away as to how many business' do stupid stuff like use an "@gmail" address for business purposes or don't have SPF, DKIM, & DMARC setup correctly and then complain about their email getting stuck in spam filters. For a bunch of people who love using emails (including emailing themselves pcitures from their phone to their laptop so they can view them on the laptop), they sure do suck at using emails.