A quick look actually does show that All Seeing I track did crack the top 75- it actually hit number 11.
Yes, I'm surprised nobody seems to remember it, it was a big hit at the time and played constantly on the radio. And Britney Spears covered it too on one of her albums, which was actually produced by All Seeing I.
The Pops performance is definitely my favourite performance of the Cowey era, incredibly distinctive, although annoyingly it doesn't appear to be on YouTube at the moment. It is really clever, though, and brilliantly directed. I thought it was fantastic when it was first shown and in the days before YouTube I was desperate to see it again.
TOTP did put some strange things on during the Cowey era that didn't get near the top 40. I know a fair amount of low & non-charting stuff went out during the late repeats but not the original screening too (as well as controversial stuff like Eminem, and the full Rock DJ video- one of the rare times Cowey showed a video), presumably wanting to use some of the performances they'd pre-recorded (there must be loads of unscreened ones from the Cowey era, I know some have turned up on TOTP2 down the years).
Yes, there were some funny ideas during that era, although in terms of the actual show itself they probably had the greatest concentration of Top 40 hits because there were no exclusives or anything and they repeated many performances quite a lot. But as you say, sometimes they would show different things on the late repeat - I remember one show in 2000 when they only showed two performances on the late one because they'd only entered the charts low down in the Top 40 and presumably decided they weren't worth showing on the primetime one. As you say, at that point they were also expressly recording performances exclusively for TOTP2 as well.