Travs - I think the system is OK in general and the leagues have differing rules.

WPette was a decent cross country runner and went to Bangor. The North Wales league then had rules such as:
No guest runners.
Only first claim runners could count for the team.
Had she been allowed to run as a guest, I still think it would have been tad awkward, sometimes travelling 2 hours and trying to blag a lift from the Uni mates, Menai or Eryri runners.

Had the league allowed 2nd claim to count, that would have been better for her and that could be a change enforced by UKA to all leagues, but it's not currently on the tables as far as I know.

And my daughter had received a £1500 bursary for her running ability and felt she should be running for the Uni, so resigned her 1st claim at Blackburn and joined Bangor Uni 1st claim.

Some leagues allow Uni runners to maintain their home 1st claim and have Uni as 2nd claim.

County Cross Country rules allow Uni students studying in the County to run in that County Champs and also represent at Inters if selected.

It is a team event really, and in my dealings at county and local league I've always approached it to try and help athletes have a better chance of being part of a team, such as the move to allow U20s to count as seniors in our leagues and County Champs.
U20s are often billy no mates in races

I have one issue, that's abuse of that offer for University students. I have known athletes go to Loughborough College and run as Loughborough Uni in the XC league.
Maybe it's OK and they have a joint running club , but it seemed suspect to me.
I'm sure there are a few "loopholes" used to boost the Uni team ranks.
That is something that should be better managed.