Hi Katherine,
MsDeploy is the underlying command line tool used by Web Platform Installer. While Web Platform Installer (which is just a GUI tool on top of MsDeploy) does not give you an opportunity to choose an application pool, I'm sure hosting control panels do have ways of passing extra parameters to MsDeploy so they can create and use an application pool when installing sites from the Gallery or using MsDeploy packages.
Web Platform installer seems to either assign the default app pool or the default .NET 4 app pool if the package is configured for .NET 4, but you could of course change the app pool after it installs.
Best,
Joe