I choose initially to use the "silly" variant in addition to the base, meaning I can't use this one too? Why these mods can't just add more ruins to the base mod, like an expanding library? Or should the base mod allows more than one additional mod?

This mod detects The Ruins Mod - Base (Time) and will generate them if this pack is installed and FortressRuins is set under mod options/map as the default ruin set. I can add silly to this one so it loads them also

Yes definitely, that would be cool.

I player further and with your mod replacing the previous ones, I now have only defended aliens sites, and no more the more mundane small assembly lines, abandoned cars on concrete floor and such like. It's a bit of a pity, I believe both should be able to co exist and I'm now with an explored map containing dozen of alien sites. What is strange is that I have ONLY alien sites generated now!

do you have the ruin pack called The Ruins Mod - Base (Time) installed The Ruins Mod Updated (Time fork) uses it to create the base ruins and Fortress Ruins can load The Ruins Mod - Base (Time) ruins also, I am yet to add the silly ruins to the intergration script as I am currently making a new ruins pack.

I did not, I have added it now. The whole matter is confusing must I say though, it seems there are 2 sets of Ruins mods in competition somehow. Initially I had The Ruins Mod 2.0 installed, and using the drop box I added Silly Ruins to it.
Seeing your mod, I added it, but it wanted The Ruins mod (forked) to work. I tried to maintain both mods, but Factorio crashed (same interface). So I disabled The Ruins Mod 2.0, and thus the Silly extension.
And then, as I told you, only Aliens ruins appeared.

I'm not sure why the fork, to sum up, does not have the base I expected which was present in The Ruin Mod 2.0.

So you are telling me, I think, that The Ruins mod Forked needs Base Ruins to have the same content as The Ruin Mod 2.0 ... Ok... But confusing.