Here's what you're trading for the alertness feat if you don't take the abil score upgrade and instead take the feat:
- +1 to damage
- +1 to hit
- +1 to AC
- +1 to Dex saves
- +1 to Dex checks
- +1 to init
The question then, ultimately, becomes, is +5 init (net +4), no surprise and no advantage on attacks against from hidden opponents worth it.
The latter two features are very dependent on your campaign and DM. Surprise should be a fairly frequent occurrence on both sides of combat, but that still depends on how willing your DM is to allow it or stage his monsters to have them obtain it (and kind of how cautious your group tends to be). Monsters attacking from hidden is another one that really depends on your DM, you group and how well you guys are at nosing out monsters from the shadows.
So ignoring those two items since they are DM and campaign dependent (and thus can't be weighted objectively), the question then becomes, is +1 to Dex more or less beneficial over 4 levels than +5 to init.
For pretty much any character other than the Assassin Rogue, I'd probably argue that they should take the stat upgrade early, the feat at L8 and then the last stat upgrade. However +5 init has amazing synergy with the Assassin Rogue and you're going to get a ton of mileage out of it.
If you're already at 20 Dex (if you managed to start at 20, or 18 and are at L8), then there really isn't any stat upgrade that is worth taking over this feat (though there may be better feats). Rogues are skill monkeys, yes, but +5% in a single ability set of skills is not worth the +25% to initiative and other features o this feat. The only one that would be worth considering at all is Con for the extra HP, but it's really not that many and you're better of boosting your damage significantly.
Take the feat at L4 (or even better, play a human and take it at L1).
The rules that you've quoted are pretty clear. You gain advantage when attacking unconscious creatures, and you gain disadvantage when attacking prone creatures from further than 5 feet away. If you have both advantage and disadvantage — you're attacking an unconscious creature from further than 5 feet away — you get neither, instead.
Best Answer
No
This is an instance of specific beats general. The feat grants you immunity to granting advantage when you can't see the target; it doesn't have any additional criteria for that.
For the purposes of abstracting the matter, consider that Perception isn't just a measure of visually seeing something. It also includes hearing someone moving or using other senses to detect the presence of something. From the PHB:
So a creature that's unusually alert enough to the point that they've the Alertness feat is someone whom isn't just seeing you. They're hearing you before they see you. Or smelling you before they see you. Or feeling vibrations in the wind before they see you. Or whatever else, to the point that you don't get Advantage to attack them unseen.