Thing is there are some mods I've looked at (e.g. a lot of the replacer plugins like Oriphier's) where there is absolutely nothing to include in mlox. They don't have evil GMSTs, there's no other plugins included in the download, there's no "patch" plugins etc etc. So, OK, one could create a Conflict rule for all the Umbra replacers out there but I like to think that there has to be some thought applied by the end-user. People should be aware that running two replacers for the same item are going to conflict.
If mlox was structured more like BOSS is then I could see it. The idea behind BOSS is creating a single, monolithic list of all plugins where each plugin has a single entry and that is its place in the load order list. mlox is more flexible in that a plugin can be referred to multiple times in multiple places for reasons beyond just load order. The conflict and other such rules in mlox go way beyond what BOSS offers. That, though, means greater effort is needed when creating a plugin's rules in mlox than is the case in BOSS. So, proportionately (a lot!) more mods are included in Oblivion's (and I guess Skyrim's) BOSS master lists than in mlox's rules.
I do like BOSS' approach and a combination of the two would be ideal: BOSS for a coarse sort of the plugin list with plugins grouped into general categories then a finer sort using mlox's plugin-specific rules
Don't look at me to assemble that BOSS-for-Morrowind list though. I enjoy having a potter with mlox rules now and again and that's enough for me