I don't see this has any real difference to asking for the freehold, if you have a 99 year lease isn't the value almost identical to haveing the freehold? we own a flat with a 99 year lease, it's value is still £165k despite us not owning the freehold, infact the freehold for all 20 flats in the block which is about 3mill value in flats is for sale for about 15k.
Your lease may well just keep renewing but if it doesn't once that lease hits 80 years remaining you'll find the value of your flat diminishing and the less time left of the lease the lower the value will be. That's because, theoretically at least, at the end of the lease the owner of the freehold can sell the freehold to Tesco to turn into a supermarket.
The freehold on your building at the moment has very little value as all the flats have a 99 year lease, as those leases diminish so the value of the freehold increases.
I would guess you pay service charges / maintenance for the building as well so essentially the owner can keep the freehold with little to no expenditure.
In practical terms the lease is exactly what SISU need, in this instance the lease lies with ACL so if they want the lease they have to purchase ACL, and, in the same way as when you purchased your flat the previous owner would have had to clear their mortgage using the money you paid, I would expect the loan from the council to have to have to be cleared.
The only advantage to SISU that I can see in owning the freehold is that it would be easier to secure borrowing against than a lease. It would also mean they could, if they wished, do pretty much anything including chucking CCFC out and knocking down the stadium part of the complex. CCC retaining the freehold would prevent this.