I think the easiest answer is that, as with all the best things in life, it's probably not quite that simple.
In answer to your question
@Matt N, the 80s were a very different time to now. There are quite a few things that got planning permission during that period that simply wouldn't get through now, as planning law is much, much more defined now than it was. Effectively, this was a period before the 'treeline rule' existed.
But equally, I'm not sure how much the 'treeline rule' exists in the format of a specific rule. I may be wrong, but I don't recall any of the park's planning documents or decision notices from the council ever referring to a specific rule related to Alton Towers. But rather it's a bit of a patchwork of existing legislation, which creates that shorthand that developments at the park shouldn't be visible above the treeline/outside the park.
That said, the height restrictions were being introduced at Alton Towers earlier than the Thunder Looper. The original GPD areas were certainly defined by 1989 (though I have a niggling feeling possibly earlier than this, I seem to recall seeing a 1986 document once).
This is just supposition, but I think the 'treeline rule' might tend to be linked to Thunder Looper because the coaster opened in the same year the 1990 Town and Country Planning Act was enacted, which would have affected how both the GDPO, as well as the Alton and Farely Conservation Area, was enforced. The GDPO effectively limits much of the park development to 5m for buildings and 25m for rides, but I think it will be the enforcement of the conservation area which results in the 'treeline rule'. (i.e. to protect that character of the conservation area the rides should not be visible outside the park)
As an aside, it was actually Forbidden Valley's 'planning permission' that put the writing on the wall for Thunder Looper. In the agreement that allowed Forbidden Valley to become a GDP area in 1993, one of the conditions was that Thunder Looper had to be removed by the end of 1995. Clearly this was extended by a year, but Thunder Looper had to go to allow Forbidden Valley to exist (and potentially also as part of Nemesis' planning permission - the language is a little unclear).
Incidentally, it turns out it was this same agreement that resulted in planning permission being required for Project Ocean. You'll recall there was a lot of confusion as to why that planning permission was sought for a ride under 25m within a GDPO - but actually the Forbidden Valley GDPO has 'modified rights', which means that rides over 5m tall require planning permission, as well as any development that result in the removal of trees.
