I've never heard of the rule either, and totally confused by the set up never come across a surgery with own dispensary and bolt on pharmacy!
I can only imagine that if they are using this rule, the purpose has to be that the surgery covers a town and rural area with is reasonably large, so it carries a limited dispensary for patients who when the pharmacy was closed would find it difficult to return at a later time/date to pick up their prescriptions, so stocks would be very limited.
If the actual pharmacy is a blot on to the surgery, I would suspect that the surgery dispensary actually get their stock from here, and the pharmacy will have an 'repeat prescription' ordering facility. So I would ask the pharmacy (and if necessary your surgery) if you order your repeat via the pharmacy, that they pass it over to the dispensary for you to pick up..
If not, I think I would pick up my script, then pop it into my nearest pharmacy to where I worked...