Shortest answer first: use overlays or sprites.
Now the explanation: the best thing to do in such cases is: you have a basic map without transparency and then put different maps with transparency on top of each other, one for each building in the current state. Sprites work the same way, but they aren't whole maps, just the buildings, and then just have to be placed in the right place. Sprites are more flexible because you can put them anywhere, overlays are just different images on top of each other.
After the explanation here is the sad truth. I have no idea if this is easy to do with RPG Maker or at all, it depends on the commands the API provides.
If I remember correctly, there are two event commands called showPicture() one for the screen and one for a specific image, both commands contain, if I'm not mistaken, a parameter like trans, opacity or something similar, which indicates transparency suggests. You can try that first.
If it doesn't work, there's still the hardcore way of using your own plugin. Of course, for this you need knowledge of how to create a plugin for the RPG Maker, and of course in the appropriate programming language, I think JavaScript. And last but not least, you need documentation about the API, the interface that RPG Maker provides to the plugin.
Here is a brief note on the general approach.
First try the internal options for an hour or two, if the result is useful use it, if not forget it or deal with the plugin problem. Find documentation about plugin importing and programming and read through it, even if it may seem difficult and you don't understand everything, do it. If you don't manage to keep it up, you won't program a plugin either, experience is valuable. When you're done, think about the cost-benefit ratio. Then decide.
Here is my personal experience in software development.
If you are not 100% sure that you want to take the difficult path: don't do it.
If you use the approach as described above, you lose a day and can then adapt the design to the possibilities of the engine. If you go the difficult way, there is always the possibility that it won't work because the engine doesn't allow it or you can't do it. Then, when you find out after three to four weeks, you'll get frustrated and lose all fun.
So the very last question you should ask yourself, a small success and fun doing it or frustration and the result you would have gotten anyway.