It is typically the best choice, yes. It's instant, you can use it whenever you like. Want to use an Ouros portal? Gotta disable, say, Afterburner first, or flight, or not be mid-port. Want to use the slash command? Instant. You're there now, no need to disable any powers to do so. Hell, you don't even have to have any HP to use the slash command. You can do it while you're dead, or untargetable, or anything. Your status is irrelevant, you can just instantly pop over to where you need to be. That's not the case at all with the Ouroboros portal.
If those people have it down to a science and aren't using the slash command, which is indisputably the best option for the majority of scenarios, then they don't have it down to an exact science, plain and simple. It isn't rocket science: Instant, no interrupt period, access to far more zones than Ouroboros has access to, available starting from level 1, where as you can't use your Ouros portal yet at that level, able to level up with NPCs in the base or sell your extra enhancements recipes on your way to porting out extremely conveniently.
By your own admission, in some scenarios, the Ouros portal is -on par- with the slash command. I can think of maaaybe one or two scenarios in all the TFs/mission arcs where Ouros is preferable, and that's specifically for TFs that want you to talk to Miss Lib in Atlas, or Azuria.
If you want to go to a hazard zone? Slash command is better. Unquestionably. You got people in your group who get lost in transit trying to get to places, like, say Posi 2, how everyone blanks when it's time to go to Faultline? "Hey, just type in /enterbasefrompasscode portal-1111 and take the Faultline portal." Boom. Easy directions. Ouros, you'd have to walk them through "Oh, well, first you take the Ouros portal to... oh, well, I guess you can't get to Skyway from there, so, uh, I guess go to Talos, then take the tram to Skyway, then go down to the Faultline entrance?" or at best "Hey you already bought the Pocket D porter I hope, so just use that, then go to the Faultline elevator."
It's just better. Yes, as you said, the Ouros portal is better at taking you to Ouroboros. Yes, in one or two instances, the exit is preferable for time over the base exit point. Otherwise, it is, in a couple instances, on par with the slash command, and in most instances, no where near as effective.