This is what happens when responsible parties don't work together and instead start pushing their own individual agendas. An incompatible mess where everybody loses. 
Ultimately this is my complaint.
I'm not a programmer, or a ROM hacker, I'm just an end user. So my gripe stems solely from the fact the we have different entities (ROM providers, patchers, hackers, flash-cart producers, mapper makers, etc), and each is producing something which should be 100% compatible with another, but is not for whatever reason. Or it was compatible, but then one group decided they wanted to use another system, and suddenly everything is out of sync.
Planetemu was a great source for clean ROMs, what they provided worked. It worked with what RHDN provided. But now they've changed it. This means RHDN either needs to change all its patches, or I need to find another ROM supplier (I chose the latter). Even if RHDN did update all its patches, what about those acquiring headered ROMs elsewhere? Why must there be so much confusion? The emulators I have will boot headered and unheadered ROMs in exactly the same way, so what is the logical reason for changing a system which we've become ingrained with.
I mean, to put it another way: a metric time system (100 < 100 < 10 + 10) makes more sense than two lots of 12 hours, but we're never going to adopt metric time because we're ingrained with what we have. This change to unheadered ROMs, even if headers are junk, seems to be creating more confusion and chaos than actual benefit. Actually, I can't see that there is any benefit to it at all. At worst headers are superfluous and vestigial/uneeded. You don't notice. But remove headers, and at best no one notices. At worst, the ROMs refuse to work, patches won't work,
nothing works! I managed to get around this ROM problem, but I had to work at it - reading through README files, patching and then checking and then redownloading and then patching again.
Why couldn't the PCE games I patched just work, off the bat? That Bubblegum adventure game at least had the decency to provide two patches in the ZIP file, one for a headered ROM, and one for an unheadered version (well done to the team behind that - I noticed and appreciated the effort you made). Most of the other games didn't even acknowledge that there were two different kinds of ROM. A few just said "get a clean ROM". Which is what I assumed Planetemu carried! At least, they once did....