Setting an application to run as an administrator directly through the properties of the executable itself is there so that no matter what, the executable will run as an administrator when launched.
Setting an application to run as an administrator through a shortcut means you can have one shortcut that runs a target app as an administrator and another shortcut that does not.
There's a setting within VoiceAttack (way in the back, last tab of the Options) as a convenience feature so that Ma does not have to dig through the above-mentioned properties to run as an admin (if absolutely needed).
VoiceAttack starts off with these warning messages as an indication that if things do not work, you might want to consider running it as an administrator. Essentially, 'Hey, if you're using VA and certain things do not work on your machine, you might want to try this.' This is in direct response to many users running their target applications (like E:D and Star Citizen) as an administrator (for almost always the wrong reason or no reason at all), and then either writing lengthy emails/forum posts/reviews about how VoiceAttack does not work no matter what they do. What is actually happening is Windows is preventing VoiceAttack (or any application not running as an admin) from accessing an application that IS running in an admin security context (again, probably for no good reason). Most people do not understand that this is actually a thing that Windows does to protect you from rogue applications as there is no message from Windows to the user when the access fails, and there is absolutely no indication through the API if the input is blocked that can even be relayed by VoiceAttack. Adding code to check if the target is elevated and will not receive input adds way too much overhead and would add a significant performance penalty for the majority that do not need it (requiring yet another dreadful option to disable the check somewhere, which in turn would require some kind of warning message at startup about what to do about improving substandard performance o_O).
Given all that, the simplest thing to do was to just let the user know what could be going on if things aren't working - add some kind of warning message at startup that the user can choose to close (btw, messages that do NOT show up if VA is already running as an admin - which is why one would see the messages when VA is not running as an admin). As an aside, the warning messages have pretty much eliminated the stream of emails/forum posts/reviews, and has been in place for probably a decade or more now. To be straight up, this is the first time I've heard about anybody having any kind of difficulty with this method. I'll take it under consideration going forward, as this could just be the first of a lot of people having the same problem.
Thank you for bringing this to my attention and I appreciate the suggestions. Glad you're up and running now