I am afraid the answers to all of your questions are no.
The 2 bosses having a conversation shows up in game, but is not possible with the current MA limitations. It is also one of the most requested features, so we can hope it will be added sometime in the future.
You can sort of fake the clue for the collectibles, but only if all of your glowies spawn in the same place every time, which there is no way to guarantee. If you want 4 crates, create an objective named "Crate" with three instances. Put in the plural and singular navbar text and set them to spawn in the middle. Create a second objective named "Crate " with one instance, with the exact same navbar text and set it to spawn in the back. Just put the clue info in the single objective.
Assuming that the Middle and Back locations are not reversed (Which you should check on any map when glowie or boss encounters need to take place in a certain area.) the players should find it last and get the clue after touching all the crates. Unfortunately, because spawning is random, even if the map is correct and your settings are correct, it is still sometimes possible to have the glowie with the clue show up before some of the others.
The only thing we can do with the standard mobs is change their colors. (Which is extremely useful and can help out your story a lot.) We can't do anything with their powers or add any lighting effects like glows or auras. Depending on the group, you may be able to create a reasonable facsimile with a custom critter. Most of the other groups in the game are pretty doable, as long as they don't have robes like the CoT or backpacks like Goldbrickers or Arachnos.
Justice Blues, Tech/Tank, Inv/SS
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Fighting The Future Trilogy
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Another possibility for your collection question. If your only objective on that mission is the collections, you can use the mission complete clue. If you have other objectives, you could also have the first collection clue be a reminder that you need all four and will look at them after the mission is over, and again use the mission complete clue (which also has much more text space).
Just getting my feet wet with the MA, and I have a couple how to questions? is there a way to:
Always make two different bosses appear together? (Preferably without killing XP)
A way to trigger ambush on elevator exit?
Have a clue pop up after ALL collectibles have been retrieved? I tired, but the clue appeared after first one was collected.
Use a custom power set on an existing NPC skin?
Add an aura to an NPC skin?
And one for Wish I could have, a way to set the custom abient sound of a map