(See the best response by Tom.)
So I've created this launcher for Kaizoku which works perfectly but each time someone uses the START game button, the game starts (using the link() proc to launch the game.) But the player is connected as a guest key even if he's logged in on his BYOND pager. Any reasons why it works like that? O.o

I'm asking because this is not a programming issue with the launcher since it works fine without having it wrapped with the BYONDexe tool. I'm pretty sure the issue is from the standalone itself. :/

Download and test from here:

EDIT: a link to the launcher made in DM codes without being wrapped with the BYONDexe tool works fine:
Best response
The standalone is meant to be independent from the pager, as the whole idea is that you can distribute it to users without them having to go through (or even be aware of) BYOND. However, you can use the configuration to support logins (and signups) for a BYOND key through the standalone interface. You would want to disable the auto-login as Guest for this. The keys are stored in the same directory as regular BYOND installs so they would be able to use their existing keys too.
Ohh okk ...

What if I want the launcher to launch right away AND have them automatically logged in without having the players to go threw the standalone interface?

Since the launcher is single player, I dont need the standalone window where it shows the list of online servers and an option to launch the local file. :/