I've noticed that the default installation directory scheme varies from installer to installer.

What made me first notice is when one package defaulted to...
C:\Program Files\CoffeeCup Software
then it preceeded to install in the root of that directory, not a sub directory as expected.
In the Web For Builder it fully specified the default directory with \CoffeeCup Web Form Builder
So when Visual Site Designer defaulted to the root directory, I added the browsed to the desired subdirectory and installed. It then created another directory in that directory.

I don't care which method is used... I'd just like it to be consistent.

All of our software installs into C:\Program Files\CoffeeCup Software and then creates its own folder based on the application name. The only exception is our HTML Editor which installs into C:\Program Files\CoffeeCup Software

Examples:
C:\Program Files\CoffeeCup Software\CoffeeCup ShoppingCart
C:\Program Files\CoffeeCup Software\CoffeeCup Visual Site Designer
C:\Program Files\CoffeeCup Software\Direct FTP

Sometimes it asks if I want to install in Program Files\CoffeeCup Software and then it creates a sub directory. Then other time it will ask if I want to install in Program Files\CoffeeCup Software\program-name.

As for the HTML Editior, I am curious, why does it install in the root and not in it's own subdirectory?

The reason for the editor installing there is for compatibility. Sort of a 10+year issue that we are stuck with because the first version of the editor installed into that location (we only had 1 program then).