The real argument in favor of separating them, is that if I'm making a Dragon Disciple, I don't have to wade through every Monk thread to figure which one is a Dragon Disciple one and which one isn't.
I can save you some trouble.
My take on the DDM is, just run it to get the PLs done and never look at again. ChrisTheMiss goes into more detail
here, but for the most part, my thoughts mirorr his.
The Dragon Disciple isn't worth putting serious effort into specific builds for it. This is coming from someone who runs their TR builds generally as the class/iconic/archetype was intended.
I'm on my third TR of it right now and it's been the least enjoyable to level of all the archetypes. It gets even worse in epics due to lack of supporting destinies, caster level scaling, spell selection, etc.
It is essentially 1/2 of melee monk combined with 1/2 of a warlock-style caster. For whatever reason, mashing those two parts together seems to add up to 3/4 instead of a complete 1.
Then there is the worst part - gearing. DDO's gear design pardigm is extremely hybrid unfriendly. It's a royal pain to gear a hybrid properly.
I ran my first DDM life as a melee primarily. If you do this, the DDM's AoEs and SLAs are so underpowered they're not worth using so you're essentially stuck on a weaker version of a proper melee monk.
I ran my second DDM life as a caster with a bit of melee. This is likely closer to the true intent of the archetype. It levels better than the melee-centric DDM due to the AoEs being semi-useful. However, the AoEs still felt underpowered versus other casters, even versus a warlock. It doesn't hold a candle to sorcerors, druids, etc.
For the third TR, I'm basically just doing the caster-centric version again solely because it clears trash a bit faster than the melee. At this point though, I'm just doing it to get it done and TRing out of it as soon as I hit 20. For whatever reason, it just isn't fun to play.
For the record, I've run plenty of hybrid builds for TRs in the past and find many of them enjoyable. One of the best was a staff-based Sacred Fist/Rogue/Monk hybrid that was a blast to play, even if it wasn't a meta build.