My applications share an X11 display, and if I'm not mistaken, they are pretty well isolated from each other. (Are you referring to MicroSoft Windows[TM] by any chance? Yeah, that's different.)
(they have essentially written 2500 lines of c that acts as a proxy of sorts)
If I was worried enough (I'm not), I could use multiple logins. Two different X servers under different users would be completely isolated.
By the way, they may have an history, but nowadays I wouldn't bet on the security of the average distro vs Windows, and I say this as a dyed-in-the-wool Debian user. For example, their Desktop environment does have protections against cross-application attacks, unlike X.
You are probably mistaken.
https://github.com/esonn/x11log
http://blog.martin-graesslin.com/blog/2015/01/why-screen-loc...
You might want to look at qubesos :