Remarkably the base unit Does gain the ability when learned in another form, but the summon form does not. And actually the initial summon counter does not pause if it enters another form and will bump you back to base regardless of time remaining on the second transformation. Everything is going fairly well, this is interesting stuff to work on, with one exception... I have 3 transformations for the base unit, all made from brewmaster ability. i have set their button locations so they dont overlap but it seems to be random which one activates when i press any of them. i thought maybe it was ranking them by proximity of the 0,0 space, but some went up and some went down. i had 3 guys all attempt the same transformation and literally got one of each of the possible three. do i need to recreate the others off of a different base ability, or...? whacky stuff
Whenever you tell a unit to do something you issue it an Order. Abilities are no exception and have their own Orders.
You can see the Order String of an ability on the ability itself under Text - Order String - Use/Turn On. Other Order String types can be found here as well.
You
CANNOT modify this field, despite appearances. It's something that should've been fixed ages ago.
So for example, Storm, Earth, And Fire uses the Order String "elementalfury" .
(why this isn't called "stormearthandfire" is probably because the ability was originally named Elemental Fury during development)
So when you click the Storm, Earth, And Fire ability the unit is issued the Order "elementalfury", which then tells the unit to cast any ability it has that uses this Order String. But in your case you have multiple abilities that use this Order String so the game runs into a problem. Units can't cast multiple spells at the same exact time so only one of these abilities can happen. Which one it chooses is probably out of your control.
Simple solution:
Use different transformation abilities. Some options off the top of my head: Bear Form, Storm Crow Form, Chemical Rage, Metamorphosis.
Advanced solution:
Use the Channel ability, which has a unique field called Base Order Id which allows you to modify the Text - Order String - Use/Turn On field. In other words, you can give a unit any number of Channel abilities as long as they each have a different Base Order Id (Order String). This ability is designed to work with triggers and has all sorts of features that allow you to customize how it functions. Setting the Follow Through Time to 0.00 and Disable Other Abilities to False will turn it into a non-channeling ability. Also, make sure that it's set to Visible in the Options field otherwise the button/icon will be hidden.
The idea here would be to trigger the transformation stuff yourself, which can be a pain to get working but can also open up the door for more possibilities.