From the days when I worked in insurance:
The upstairs buildings insurance company are quite correct that they can only deal with claims for damage to the top flat, BUT your claim is not on the buildings policy, it's on the public liability section of that policy. You make a PL claim if you can prove that the owner/occupier of the flat was negligent in failing to maintain the bath outflow so the leak arose, causing damage to your property.
What happens now is that you discuss this with your own insurance company and submit the claim to them (as the rental agents suggest) - they then deal with the claim under your own buildings insurance, but they then look to recoup all their outlay from the insurance company of the owner above. It's a straightforward process for one insurance company to claim from another - each deals with their own policyholders then sorts it out behind the scenes.
Regarding the second question - that's a matter between the tenant of the top flat and the owner - it depends on the terms of the tenancy whether she can sub-let, she may have permission of the owners - she doesn't need your permission, who lives in the top flat is nothing to do with you as long as they are paying their ground rent to you.