Me too. Without triggering a poll, it’s not even in the Top 3 of TOTP themes, but it has a real charm and somehow felt fairly contemporary and appropriate in both eras it was used (it would never have worked in the Britpop/post-Britpop years).
I always liked it too, though I would say the original version was superior to the remixed version they used in 2003. In those days, as you can see on YouTube, they often wouldn't introduce the programme over the globe but straight off the back of a trailer, and the intro always sounded quite good in that context.
Stan Appel was clearly a fan of Tony Gibber's work as he also commissioned him to do the theme tune for the short-lived Les Dawson quiz Fast Friends that he produced in 1991, and the two themes are not dissimilar - https://www.youtube.com/watch?v=fLPc4eFH6hk
Fast Friends was a big flop, in Louis Barfe's Les Dawson book Appel says the whole thing was acquired, piloted, recorded and broadcast within about three months, so it was a bit of a frantic production. I love how Les is blatantly superimposed into the titles.
There's various reasons why they could have happened. The main ones I can think of would either be connected to making it easier to share footage with the international versions, or that the cameras and the likes they were using weren't near the end of thier life and they didn't want to spend money on replacing equipment which still had several years of useful life left.
As I've said before, one issue they had in Elstree is that the gallery for their studio hadn't been refurbished since the ATV days, and so initially Pops would use the gallery from another studio, but towards the end of the nineties that studio went on long-term hire to Kilroy and so the gallery was in use every day and they couldn't use it anymore - so instead they used an OB truck parked outside the building, so it does sound like they were using rather limited facilities in the last few years. Even so, seems bizarre there wasn't a better option.
As I've also said before, Richard Marson talks in his book about filming a Blue Peter item on Pops and seeing that, as they were at Elstree away from all the other programmes, Chris Cowey had total control over the whole thing and everyone would defer to him at every opportunity - "I'll just check that with Chris", all that - and it had turned into totally its own self-contained empire.