Modern windows systems use UAC (User Account Control.) This works with a token based system. So for example you have a windows account, and that account has local admin.
When you login you will be issued a token that allows to execute programmes with your low level user privileges, thus limiting you to the least possible privilege.
If an executable requires elevated administrative privileges to run, when you lunch it, it will prompt you as the user to explicitly okay it.
When you do this windows will check if you have administrative privileges, which you will as you are a member of the local admin group and it will issue a token allowing that instance of the executable to run with higher level privileges.
This keeps the policy of most restrictive privilege in place, as your user account will still be running with its low level privileges, but the instance of the executable will have the higher level privilege, thus creating a security boundary.
The run as feature works in much the same way, except it will check what privileges the account that is being used to 'run as' has, instead of the account you are logged in as.
So if you are logged in as your normal user account that does not have local admin, but you do know the local administrator credentials, you can run an executable that requires elevated privileges with the run as features, use the local admin creds and again the token will be issued allowing that instance of the executable to run with the required level of privilege.
So rather than undermining the security boundary, it is in fact enabling the security boundary.
You can read more detail here.