Forgive me if I'm wrong, Zacs, but I don't think this is a case of a "flying freehold". I've been involved ig For Funks Sake a few times. In each case, you are a freeholder, and so is the person below/above you..... subject to various easements/covenants/licences etc.
Cake's situation is with Leasehold. I built a small block of flats once, and simply gave the leaseholders the Freehold so that they could take over the management company I had set up. and give them total control.
A lot of builders prefer to keep the freehold and take a management fee/rent. In Cake's case, the freeholder is also one of the "tenants".
What you must do, Cake, is to have the terms of the lease/management looked at professionally by your solicitor. Various laws control a great deal of the leasehold/freehold situation, but there is still freedom to incorporate conditions/costs that may be onerous to you.
All that aside... from a practical point of view, it must surely be advantageous to have a resident freeholder rather than a non-res one. Look at it this way; they are never going to ignore structural concerns as absentees might ........ especially with the roof ;o)
This arrangement can work as well as any other. It just depends on the terms of the lease. Do have it scrutinised.