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Yes, you are right new Icon will be more relevant, only when BC3 and BC4 are installed at the same time. However, you know better about the time BC4 Betas are going to continue. For that much of time different Icons will help, thereafter no one will remember.
I find that loading a WorkSpace, closes previously loaded sessions/workspaces. So, I may want to have BC3 as well as BC4 installed at the same time for a longer period of time than just the Beta Period. So, that I can have two separate workspaces open at the same time.
Further, I just noticed that there is feature to open another instance of "Beyond Compare" via "Open With" feature of Beyond Compare. In that scenario I may want to open an instance of BC3 from BC4 or vice versa.
Specifically for workspaces, you can use the /solo command line so each new launch is a separate process. Each process can then open a Workspace. You can create a new Desktop shortcut with /solo to launch a new process/window each time it's needed.
*Instead of multiple major versions, you can install a separate Portable Install of the same version for multiple installations. This would be if you need to test entirely separate sets of settings.
On my system, for example, I have my own BC3 and BC4 installs in Program Files (x86), and I also have portable installs of BC3 and BC4 on my desktop or in C:\Beyond Compare\ for additional testing/scenarios.
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