I want to run an application at startup. I understand there a few options. I'm most interested in the options below:
Is there any difference between the two options?
There's no fundamental difference. The folder tends to be favorited by users, easy for them to create a shortcut there. The registry key tends to be favorited by installers, lower odds that the user disables the program.
That's not exactly much of a guarantee anymore, plenty of utilities around that help editing the keys without having to use Regedit.exe. Including Windows' own msconfig.exe