Based on my personal experience with blind vs sighted evaluations, I believe the sighted perception that Tower speakers have a lot more to offer (when well tuned subs are in play) is very real!
However, when unaware of what the speakers look like, I do not detect the differences I did (and I thought were obvious) when I could see them!
Caveats:
1) If there is no subwoofer in play, most towers will deliver deeper bass!
2) Generally a Tower will be more efficient than the correlating bookshelf, so if you are presenting a difficult load with the bookshelf, the tower may take the strain off of your amp.
3) Often, a tower is designed to support a higher level of SPL so if you sit far away and really like to crank it, you may find/push the limits of the bookshelf while the tower is more likely capable of meeting your demand for SPL!
4) For some companies the differences between their tower and bookshelf is much greater than others. As an example, for the Infinity Reference Series, the tower is a 3-way while the bookshelf is a 2-way. However, among the JBL 5 Series, the 530 and the 590 are both 2-ways. Obviously when the design is different between the tower and the bookshelf, the differences between them are increased (sometimes that helps towers, sometimes it hurts them). Among companies that have good engineering that targets a simular sound character from their speakers, different designs will still have largely the same character.
5) The location of your towers, if you plan to run them full range, is of paramount importance. The extra bass presented by towers may tempt you to lower the crossover to the sub(s) or to keep the XO at 80Hz, but use both your sub(s) and the towers for bass. Below around 250Hz, the room is a dominant influence! Your towers may help balance and even out the bass through your room similar to adding two more subs! However, it would be a mistake to just add them in and assume it would improve the quality of your bass. Based on my informal tally of accounts of people who attempt this while measuring the results, it seems that more often than not, they simply cannot obtain better results using the towers because they cannot reposition the towers for optimal bass. It has become common wisdom when running Audyssey to set your towers as small so they are not involved in producing bass. However, there is always the possibility that you would be one of "the fortunate few"
My experience has been:
Most well designed bookshelf speakers produce ample SPL for normal listening in a typical living room (item #3 above), I use a sub (Item #1 above), and I have ample power to work with my bookshelf speakers (#2).
So I see #4 and #5 as the true "wild cards"!.