Only if you want to be able to use Indy components in a Form Designer at design-time. Otherwise, you can just create the components dynamically in code at runtime.
Yes. Though, the runtime package binaries do need to be located where the IDE can find them when loading the design-time package binaries.
Since you already compiled the binaries, you don't really need to compile them again, so you don't need to open the projects. The "Install Packages" dialog is just looking for the .BPL binaries. But yes, it would just be the two DCL packages.
None. You already created them.
Basically, you can't. But you can re-enable it when needed.
No, you can't. But you can install packages on a per-project basis. So, make sure no project is loaded, and then go into the "Install Packages" dialog and remove the Indy packages. Then, load a project and re-add the appropriate Indy packages you want to use for that project. Then close the project, load another project, and repeat. As long as you maintain the separate Indy versions, you should be able to pick which version you want to use for each project.
Of course, this is all just contingent on installing Indy in the IDE at all. If you create Indy components dynamically in code instead, then this matter becomes moot, since you can just make each project reference the appropriate Indy source/binaries folder as needed.
Yes.