This information is all supplied by a guide book I have for SA2B and Sonic Adventure, Versus Books, advertised as 2 guides in 1. The information could possibly be inaccurate, however everything in it is either correct or currently un-reported. Nothing is blatantly wrong.
The key values of interest are data on the Tiny Chao garden fruit, and on the rates eggs appear in the store.
The main site already has values for the fruits' effects on Swim, Fly, Run, Power, and Stamina but this guide has data on the effects on Belly and Mood stats (and this could easily be tested and confirmed.) They are:
The egg appearance rates are not as easily testable (by one person. Large crowd sourcing would be required to confirm statistics for this.) The guide also phrases it in a weird way. It says
When you first start up your new Chao, it is determined whether you get a Normal Egg or a Rare Egg. The ratio is 3:1, Normal:Rare. After it determines Normal or Rare, it uses the appearance and pricing chart as shown below.
The chart is then shown (It includes ring prices, but these are known, so I will omit them.)
So, in this weird phrasing, it seems that a "normal" egg will appear 75% of the time, while a "rare" egg will appear 25% of the time. Then, in that 75% or 25% of the time, it has further weighting for specific colors. This should produce overall probabilities of:
So, if these values are accurate, the moral is, Topaz is indeed stupidly rare.