I have the EXACT same problem and it makes me want to consider selling the van. We looked at the EXL which has a much higher clearance, but because my wife didn't want the moonroof and wanted the velour seats, we decided on the EX and not the EXL. These vans are not as plentiful so they had to find one from a remote dealer. It wasn't until we both discovered the ridiculously low clearance that I returned to the dealer. The supervisor at the service department was quite surprised that there was such a difference in the clearance between the EX and the EXL, and he said there was no ability to make an adjustment on the tailgate.
So the theory that Honda wanted to lower the rear end for stability, but forgot the head clearance would be affected doesn't make sense since the EXL is still ok. I wish we could file a "class action suit" and make Honda come up with a fix. Traumatic Brain Injury (TBI) is a hot button item, and none of us deserve to continuously have to duck under the "non-power tailgate" to avoid repeat "Traumatic Brain Injuries". I'm thinking it may be best to "trade in" this van and get the EXL because this is a serious design flaw, and it's unlikely that Honda is going to voluntarily come up with a fix.
BTW if you own this van and think your speaker must be cracked because you hear a popping noise, I discovered the fix. Apparently if even one leaf or twig gets under your hood and lodges near the windshild wiper, there is an intake opening for the climate control system in the same location. So even a minor noise in that area gets transmitted into the cabin through the air intake opening and sounds really loud. After opening the hood,we cleaned the leaves out of there, and things went back to normal. In my opinion this also is a design flaw. It's easier to buy a "keyboard" cleaner than blows air out a can from Office depot and use that because the places where these leaves get lodged is not easily accessible even with a small tool.