I think that if the app allows you to import an arbitrary image as an icon then its no more limited than any other paint package. In a sense its like having these icons on a separate layer in Gimp. The advantage to doing it this way is that because the program tracks these items as individuals then you dont need a layer to hold them for individual modification.

So you might have a dungeon with a store room and place down loads of crates. To do this in Gimp requires you to load an image of a crate - usually already made for you like an icon/ Then you have to position, rotate and scale them one by one and either transfer them to a holding layer or use a new layer for each. Now transfering them to a new layer prevents you from editing that crate again unless you select it and then move the selection and by using a layer for each means you dont have to do that but it burns HUGE amounts of memory to do it. Another problem is that every rotation degrades the image so you really have to get it rotated and scaled right in one go or else undo and redo with a different amount. By using a token based app the rotation, scale and position is extremely easy which is why people use them. And they don't degrade the token on a reposition or rescale because they might done from the original and built up - at least mine are. Guess I cant really comment on how other people make their software.

Generally using an token based app for putting token like things down is much easier and of higher quality. You can also snap to grids and maybe rotate about useful points instead of the corner or the middle of an image which might not be as sensible.

The downside is that the token apps don't have as nice painting functions and effects built into them. You can import / export between them but there's usually trade offs to the process.

In my opinion the thing is to know where they are at their strongest and weakest and use the app that applies to that job. Its a good idea to have a token based app, a paint package, a vector based one and also some 3D modeling ability. Having skills in one of each of them (or apps that cover more than one of those) is the best way.