Presuming you mean a single journey from holding a to holding b or from holding a to abattoir, then I am fairly sure that the answer is yes, subject to seperation as you state. If to abattoir, then check with them that they are happy to receive together.
"EU transport reg 1/2005 states in chapter 3 section 1.12
1.12. Animals shall be handled and transported separately in the following cases:
(a) animals of different species;
(b) animals of significantly different sizes or ages;
(c) adult breeding boars;
(d) sexually mature males from females;
(f) animals hostile to each other;
(g) tied animals from untied animals.
1.13. Points (a), (b), and (c) of paragraph 1.12. shall not apply where the animals have been raised in compatible groups, are accustomed to each other, where separation will cause distress or where females are accompanied by dependent young."
Given that this regulation covers road, rail, air and sea, the "transported seperately" must mean physical seperation, rather than different journey, otherwise a cargo ship would be unable to have sheep and goats, or cattle and pigs, and that would just not make sense. Also since the "seperation" is clearly to prevent adverse interaction, then preventing this by partitions would I believe satisfy.
If you are talking about multiple pick-ups and drops then come back, as it could get complicated depending on what you are doing!
You could confirm this with the Defra Animal Welfare Team on 0207 238 5907