But... ok, I apologize for my persisting on this issue
No need to apologize, you're concerned and this is totally acceptable, besides we all suffer from that. And the discussion is interesting.
Let me tell this example: I have recently played a beautiful hotseat match by using a bunch of mods, which eventually - more than 150 turns had been already played - proved to be not compatible. I can't look for any conflict between them. Therefore, the match is wasted.
But are you even sure this is a compatibility problem? Some mods already had this "crash/freeze at turn 50*N" happen, it is a very hard to detect bug, not only because it requires the modder to play 300 turns anytime he makes a change to his code, but also because this is a civ5 bug (just a guess - I never encountered it with IGE - but very likely) and therefore very hard to circumvent (rather than fix - another guess).
And even if it was an incompatibility, the problem remains the same: this kind of crazy civ5 bug is not predictable, unless your problem was not a freeze, crash or something like that but rather, and for example, the tech tree that became unusable.
There will be a lot of mods I'd like to use, but I won't, because not having any guarantee about its compatibility with other mods, I won't take the risk of starting another hotseat match the could prove broken after hours of good gameplay.
And this is a wise decision but it does not mean there is a solution. Modders are not omniscient : we are working with a bugged and undocumented platform, and hundreds of us are working independently, and most of us only have average computers skills. There is no way we can predict in advance all compatibility issues, even for the best of us, far from that. We can give clues and those of know already do it. Look at mods from myself, from Gedemon, from Whoward, etc: I am pretty sure that most of those creations have compatibility informations (I only have two mods myself but they both provide those data). But in no way we can be exhaustive and offers any guarantee.
Besides, the Spatzimaus solution is not as useful for you as you think it is...
* Green will be seen as "no problem". Well, this is true for 0.1% of mods.
* Mods such as Nights will likely fall in the red category. But does it mean it won't work with IGE? With InfoAddict? With the wonders mods from Whoward? No. It will work with those, perfectly (I took some measures for this and I suspect that Markus did too). And it is not that surprising.
* As a result 99% of mods should be yellow? Where will you set your own bar? Green mods only (no mod), are yellow-green ones only (about every mod)?
I do not think such a system would work.
If I could rely on this green-yellow-red code for some mods, well I could be willing to do some experiment, maybe I could start with a core of mods that are 'certified' and try to add other 'uncertified' mods one by one.
I think you should better read the compatibility information already provided by the mods' authors and try to understand when compatibility problems are likely to arise. I do not really believe in community education or propaganda, especially because new modders already have a helluva things to read and they won't jump on the "improving compatibility guide". Now, maybe a software could help to improve things but I do not think there would be enough users to change anything. Just using a tool to check the mod you created or downloaded sounds easy but in practice people do not bother in my experience.