Its because rune beetles seem to spawn with stats and attributes that put them right near the 3 slot to 4 slot break point. I had tamed and stabled five 170 stamina rune beetles before the publish to see if they would keep the 170 stamina after the publish (they did not). Three of the 5 ended up at 3 slot and two of them were 4 slot after the publish.
After looking at the differences between the five beetles, It looks to me like you can calculate the weighted value of the resists, stats (str, dex, int) and attributes (hp, stam, mana) and add them together. If the total is over 3700 it will likely be a 4 slot rune beetle. If the total is under 3700 it will likely be a 3 slot beetle. I have not tested the exact break point so it might not be exactly 3700, but its got to be pretty close to that. This 3700 would only apply to a rune beetle, because I'm ignoring the special abilities that it has since all rune beetles should have the same special abilities and other animals have different special abilities which would change things.
If I'm not mistaken (and I haven't done a lot of testing yet), it seems like the ideal rune beetle would add up to around 3690 or so such that you would have the near maximum total for a 3 slot pet thus allowing you to maximize the use of the points you get for the 4 slot and 5 slot training levels.