I like the mod, but I have problem with the "repair mission" (or how ever it is called). I am using a lot of mods and I need my time to develop. All the time a request chest occurs, which destroy my base is really annoying. Is there a way to disable it?

Yes, use this console command: /c remote.call("msi","explosion_risk",0)
Also, when you start a new game you can set explosion risk to zero.

What about the another annoying feature when bots explode flying over the glados crash site? Was this introduced intentionally, or is it some sort of cover for unsolvable game mechanics issue? This "feature" is even more frustrating since there is no way to control where the automated bots will fly. So how am I supposed to work around this?

When I develop, ideas came and go.. on that occasion, I thought of a good bonus recipe, but there is a penalty. You just have to try to work out that problem. And this recipe is optional

Actually, I do not use those special recipes since I used to build around the main bus all the times. So those sites are just few lonely shipwrecks located somewhere between outposts and the base. And when the bots occasionally fly over those wrecks sometimes message pops up saying that they crashed there.

As a general note regarding this I would recommend not to rush implementing the ideas, but double-think of their gameplay value in the first place. Try to estimate their effect on the player experience. The bosses you introduced are just awesome, I was truly amazed! That was something fresh, new, interesting, challenging. The hold'n defend missions impressed me too. The new science recipes with characters are somewhat interesting as they bring new type of small-scale puzzles, but it is not for those who build a megabase. But the breakdowns and crashes are totally bad idea, it's like ants in a pants, those "features" do not add any good to your mod - like if they were added just to annoy and frustrate. Personally, I suggest to get rid of those. Just my opinion.

I understand. Specially for megabases. In factorio, each player has a very different style of playing. Some like megabases, others dont. Some like biters, others hate them. It is very hard to please everyone. So I think the best solution is make mod options. So everybody has a chance to play a game he likes more.
Lets make this a mod option soon ok ? just like the explosions and worm boss are optionals (ahh and yes, there are other guys that hates those bosses too)

That would be perfect, thank you! I am just surprised that someone may actually like to lose bots and waste random resources due to crashes and breakdowns... Anyway, I guess it is a beef for those who play micro, a stage which I past by many playtroughs ago. :)

So regarding those options you decided to introduce... May I put a suggestion there? Um, it feels like the breakdowns deserve an ADDITIONAL checkbox in the mod startup options, since there are a lot of related Freeman's researches to counter these, which makes no sense if the risk set to 0. So the startup setting should also disable those research options in the tech tree as well.