I guess I'm either still confused or we're talking about this from two different perspectives.
I'll try to make things more clear, assuming that the confusion is my fault.
I have programs I wan to use that require root, timeshift and pacman. They are common programs that either an admin/root user or the user of a single user computer would use regularly. It would odd for someone to not execute them on their own machines. They would need to either enter a root shell with su or launch them with sudo to use them.
I wanted to streamline the process of querying for pacman updates, updating and ranking my mirror list, creating a timeshift snapshot, running pacman updates, and then cleaning up excessive snapshots. I could just manually enter all those commands through the terminal, using sudo, or I could write a program that does all that and responds to the prompts for me (we'll just ignore the dangers of "yessing" through pacman prompts for the moment). I guess alternatively, I could SETUID 0 for both timeshift and pacman, but then that means that any process could execute them regardless of current priveleges. I could also just SETUID 0 on my own program, effectively achieving the same result as what I'm doing now.
So, if it's acceptable to run "sudo pacman -Syu", then why is it not acceptable to have the program check if the user who owns the process is root, and if not, launch a new instance with "fpSystem('sudo pacman -Syu')"? As far as I can tell, it is effectively the same the concept.
In general, I wouldn't have the user/myself run something with elevated privileges where it isn't needed. I wouldn't require elevated privileges without tightly controlling what the program is able to do, and I would drop privileges as soon as they're no longer needed. I'm definitely not allowing the user to have arbitrary code or scripts run while they or the process have elevated privileges. It's controlled (to the best of my current knowledge), concise, and does no more than it needs to do before dropping privileges and halting.
So, why would it be acceptable for a user to "sudo pacman -Syu", but it would not be acceptable for my program to to execute that command given that the same user would still need to provide that root password or already possess root privileges? Why would it be acceptable for pacman and timshift to require root, but not my program?
Aside from that, though, I guess I also wasn't very clear in how I asked my question, because I wasn't specifically concerned with the dangers of running under root privileges. I was more concerned with there being any dangerous or wonky behavior associated with having the program launch a new instance of itself with fpSystem(), or using fpSystem() with root. It's a given that anything with root privileges can do whatever it wants on the machine, and that it's dangerous and unnecessary to allow it all willy nilly. I just didn't know if there were any gotchas regarding fpSystem() or any other method of executing/interacting with external processes, like TProcess, RunCommand, etc...