- when ticking the box 'Create a new secondary installation' an invalid pop up msg appears complaining that the folder is not empty, and the installation cannot continue;
More details please, I can not reproduce.
This happens when you create the installation folder beforehand and already create a new folder inside (I admit, not something everybody would do). I choose to create a new folder and already copied some custom packages in there so I could include them easily. Seems that ticked off the tick box 
But then it is not empty, so the message is right.
Yes It could have an ignore options. Currently falls under patches welcome.
However I have a couple of Lazarus versions on my PC. Will it delete/uninstall all versions and all config folders (individually set with the pcp option)? That's what makes it scary to choose this option.
Also, if I'm not mistaken, Lazarus does not misbehave by adding to the DLL hell like many other (windows) programs do. So I can simply uninstall a Lazarus version by deleting the installation folder and config path. The one shortcut I have in my quick launch bar can be easily deleted as well.
About dll: QT there is one dll.
About config: By default it deleted the config in the %APPDATA%.... folder. But if you do a 2ndary install (or actually update), it should delete the config in the folder of that installation.
It does not read pcp from shortcuts. It looks for the lazarus.cfg file.
The option originally was added, because sometimes people messed up their install, and uninstalling did not help, as config remained. So the target group usually only has one config.
Yet, I agree, if you are updating a 2ndary install, it could show the path, of the config, that it will delete.
You can add a feature request, but again more than likely: patches welcome.
I know it is.
But it would be cool/look professional if it actually were a hyperlink.
Well yes "would be"...
About the installer and it maintenance: It has somehow ended up on my list. Well mainly because there where a few things that I r*wanted* to be fixed. And 2ndly because I wanted to add the 2ndary installer.
For all else, I have enough other things that I prioritize much higher. So except for really bad bugs ("format c" kind of stuff), I will likely not do much work on it. (hence all the "patches welcome")
If any one wants to pick it up. It would also be nice to have a tool, that detects all files that were moved, and builds a list, of all ppu in the old place. This list can then be put in the installer, and the itnstaller can clean such old files (those must only be files that were actually installed by a previous installer).
That would make updating without uninstalling safer (I did such a list by hand for 1.0.0, but not doing it now)