Yep!

Apple's standard UI decision is to hide them, and for the very few who do not and who diverge from Apple's UI decision, you are now instead making it show for all of the (more numerous) rest who do honor Apple's UI for /opt, /private, /usr, etc. and they get this random /opt folder showing!

If you had originally honored the existing chflags setting for opt, you could check and then keep it so, but now you have revealed it for everyone.  Perhaps you can still do that , so anyone who has to keep running that command can run it once and then you can honor it going forward?  On the other hand, I'd say anyone breaking Apple's UI and showing it, knows how to get to it (and probably does) via Terminal, but I can see how that might be swinging the pendulum too far in the opposite direction...

That'd make it hidden, even for folks that don't want it to be.