This is very true and one has to wonder why exactly certain rogue feats exist as written. For example:
Longsword Finesse:
Prerequisite: Eladrin, rogue
Benefit: You can wield a longsword to deal Sneak Attack damage and to use rogue powers that require a light blade (you still cannot throw the longsword). You reduce Sneak Attack damage by one die when using a longsword.
and...
Tunnel Stalker:
Prerequisite: Str 13, Con 13, dwarf, rogue
Benefit: You can use any rogue power that requires a light blade while wielding an axe, a hammer, or a pick with one hand. You reduce Sneak Attack damage by one die when wielding one of these other weapons.
Now, for the first feat its far better to take Weapon Prof: Rapier, sure it can be used as a versatile weapon... but you do full SA damage with it!
In the second at least you could snag a Crag Hammer or a Waraxe to do more damage when you don't have SA, but again, a rogue that is gaining CA and using a Rapier is going to be doing more damage.
Its almost as the designers want to allow you to use alternate rogue weapons... but to always have daggers and rapiers as the best ones (and Doubleswords for whatever reason...)