On use trinkets always have had a shared cd before another on use trinket can be used. Your best bet is just deal with it till you can replace one with one that isn't on use.
You can still put them together on the same macro since trinkets are not on the GCD. You just have to press the macro again 20 seconds after using the first trinket in order to use the second one.
I'm fairly sure that the sims already factor this shared CD thing, and they will use Trinket 1 first, and delay Trinket 2 by 20 seconds, so even if you're simming the same two trinkets, you might get different results depending on which trinket went into which slot.