There are certain advantages to not installing in
%programfiles%. One is to safeguard the program from being used as a trampoline for malware (for more details see, for example http://foundstone-dire-detect-insecurely-regist.software.informer.com/1.0/ or google for more "Foundstone DIRE").
Another advantage would be to install w/o requiring elevated privileges. This may be important, again, if a program is compromised, it won't have the access rights to compromise something else.
In Linux world, it is common practice to install third-party and system's software packages separately. For instance, while usual software packages go into
/usr/bin, third-party typically goes into
/usr/share/bin if it needs to be shared by multiple users, or into
$HOME/bin if it is supposed to be used by this specific user. Hearing how it's a consultancy firm that installs these programs on your PC, they probably have some (not to say contrived) user policies which make it necessary or at least more convenient to not use