Actually, from how I understand it works, keeping them split is exactly why it gives us more options in the first place.
To create a character, you pick the race/clan/gender, then the basic face, then the details.
Each face always has six options for eye shape, four options for the mouth, etc. - the face is different but the number of options never changes. (ie. I'm assuming there isn't any space, programming-structure-wise, to add more options for any one face.)
BUT for each of those faces, the options are not exactly the same. Nose #5 on face #3 will not have the exact same shape as nose #5 on face #4. But you can't mix and match the appearance of one onto the other, it can only be used on that particular face.
So every additional face gives you another set of options, so 'merging' Midlander and Highlander would do nothing except cut down the overall amount of faces available. (Also, Highlanders have completely different models and animations - functionally more like a separate race than another clan of the same race - so unless they can add an option to let you choose between the sets, you'd lose that difference as well.)
The only possibility for expansion is whether there's a definite limit for how many basic faces there are - unlike the other settings with a consistent number of options, the number of actual faces is higher for Midlanders (6 male, 5 female) than for the other clans/races (always 4). (Giving Hyurans a total of 10/9 options per gender instead of 4 for the other races.)
Perhaps all races could have six. Only the programmers know for sure. But even if they could give that increased number of characters, we'd only get one extra Midlander face out of it and all the other added variety would go to the other races.
For other races, removing the sub-races wouldn't affect the number of faces available, but it would still lose a lot of other variation that distinguishes the clans - different skin colours, unique eyes (Sunseekers' slit-pupils and Dunesfolk's 'no pupil' appearance), Au Ra scale colours, and varying customisation options - eg. Wildwood Elezen's earclasps vs Duskwights' unique tattoos, presumably stored as the same data. Also all the lore attached to those different clans.