Turns out the reason is kind of stupid.
Back then, we didn't have usage statistics so making tiers was a heavily arbitrary decision based on each Pokemon's usage and all-around usefulness in the metagame. At some point the standard UU power level (let's call it that) was set around metagame staples like Electabuzz/Scyther/Vileplume/Fearow/Golem/Hypno, of course this was completely arbitrary.
BL was basically the UU banlist, and it included mons like Alakazam, Dodrio or Rhydon which were definitely not OU, but deemed "too strong" for the perceived UU metagame power level.
Some tournaments around 2003-2004 (for example Summer Freedom) had a weird format where you could use one BL in your UU team. In the following years there was much debate on this issue, by late RSE it was settled that BLs were completely banned.
Basically people really liked playing Fearow and Golem so Dodrio and Rhydon were banned because of that.
AFAIK Kangaskhan evaded the banlist and remained in UU forever, despite it being the most powerful mon in the meta.
So I guess they just banned a bunch of random Pokemon and both Kadabra and Alakazam happened to be banned.