All of my spells on the GCD, fire off in the order they are listed.
The click macro, calls all of the castsequences, but because of the GCD and wow executing top down, only the first spell on the GCD fires off.

Flame Shock, then Lava Burst, then Chain Lightning, and finally Lightning Bolt.

However, any spell or ability not on the GCD, fire off on the first click.

It is extremely easy to test this in game.
Just add the /use 13, /use 14, and Elemental Mastery, to say your Lightning Bolt fall-through spell.
Then have the button and trinkets visible on your bar, as you go through the macro.
Observe when they are used.

Click functions the same as one huge macro.
/castsequence Flame Shock,,,,,,,,,,,
/castsequence Lava Bolt,,,,,,,,,,,
/castsequence Chain Lightning,,,,,,,,,
/cast Lightning Bolt
/use 13
/use 14
/cast Elemental Mastery