It's a bit more complicated than that...
(And the 9999 alone shouldn't work)
First I'd say, read both links @OSUblake has posted, they are crucial. Then, read the docs about perspective:
The key gotcha is the fact that setting 'perspective' in CSS (in this case GSAP) creates a new stacking-context on the element but visually affects the children.
You have a perspective set on the 'td' element of your table, that creates a stacking context on each 'td' element that is independent from each sibling. All children of those 'td' are contained within each context and can't possibly raise higher than it's parent's siblings. Think of each sibling stacking-context as a mini universe in its own, independent and unaware of others.
As it pains me to say, it is expected behaviour.
I am not sure what is the end result that you are after but, in order to have the blue box on top of all the other green boxes and have some perspective distortion, you need to plan where your stacking context is going to be.
Here's a fork of your pen with a hack to make it work.
ps (opinion piece): It really is silly to be putting z-indexs on the thousands.... If your stacking context is wrong, it won't make a difference if you have z-index:1 or z-index:3,000,000 - If anything, it's a lot easier to keep track of the z-index if you are in the single digits. If you need more than 10 levels within one context, you might want to re-think your strategy.