I just finished researching this exact question (thanks to some folks here who provided some of their expertise offline, I'd give credit but don't want to attach their name in case I got something wrong and they get the blame for it). What we all know is that the
GiPro is an easy way to extract more power from your bike, what most know is that it does this by tricking the ECU into thinking the bike is always in 4th gear, what I didn't know was how it gains power by making the bike believe it is in 4th gear, so I dug into it a bit. What I found was that there are two things that change within the ECU when you are riding in different gears, it pulls a different map for the secondaries and it pulls a different map for the ignition timing. I'll go through both of them here, it may shed some light on why some people aren't experiencing the "wow" factor when installing the GiPro or when they physically remove the secondary butterflies.
SECONDARIES -
For whatever reason Triumph decided to install a secondary throttle in our beautiful machines. This whole thread has been discussing what exactly these do, I will not go into an explanation of that, I only care about what GiPro does. When you look at your ECU maps (in TuneECU, that's a whole other thread) you will notice a special setup for the second throttle. The map settings are based on RPM and what gear you are in. The majority of the tunes (I'll get to the minority in a second) have partially closed secondaries in gear 1-3, by GiPro tricking the ECU into thinking it's always in 4th you have 100% open secondaries all the time. This is good but not the entire solution to removing the factory torque limiter. For those who have not experienced the "wow" factor when installing the GiPro it could be that you have a tune loaded that restricts the secondaries in ALL gears. I went through some of the more common maps and found these that have restrictions in all gears, this is by no means a complete list so you may want to have a TuneECU person check yours for you (ideally you should load TuneECU on your computer and take a look even if you never connect your bike, it is a good learning experience to dig inside the maps). You can't tell what tune is loaded on your bike for sure without connecting and actually looking but you can take an educated guess by going through the list here
OEM_Tune_list and finding the best match to your bike. Here's the short list of tunes that have secondary restrictions in all gears:
20149
20223
20225
20226
20228
20256 (R3T)
20352 (R3R)
20355 (R3R)
20366 (R3T TORS)
If your bike's tune falls on this list you will not receive the full benefit (some tunes have full restrictions in all gears, some are partial restrictions in gear 4 and 5) of a GiPro without changing your map and/or physically removing your secondaries. This partially explains why some captains aren't getting the big "wow" factor that others are experiencing with the GiPro.
IGNITION MAPPING -
The other factor in the GiPro magic is the change in ignition timing. Again, I'm not going to go into the whole subject of what this is, there are other threads that cover this, I'm only concerned with what the GiPro is doing. In your bikes map there are three ignition timing tables, what gear you are in determines what table the bike uses. I1 is for first gear, I2 gears 2 and 3, I3 is for gears 4 and 5 (Note to TuneECU users, you have to load the latest version 1.9.7 to see this correctly, previous version have it wrong or incomplete). This is where Triumph really restricts the power in the lower gears, if you removed the secondaries on your bike and think you did what the GiPro does you are wrong, there's a lot more power waiting to be tapped in these tables. This is the real benefit of the GiPro's ATRE function, tapping into the I3 table all the time will certainly increase your power output.
CONCLUSION -
First thing in the conclusion, as it has to be said, once you have gotten your bike to lose the restrictions of the secondaries and the ignition timing you really should get a dyno tune to really tap into the power completely. GiPro is great for the rider who just wants to keep it simple, easy install and instant power gains (with some exceptions) with the benefit of keeping the ECU program at stock settings, a gear indicator, and the ability to turn off the power gains by pressing a button (great in rainy conditions). For those who want to dig further and get the gains of the GiPro on the cheap, explore the TuneECU option and tap into the power yourself. Hope this helps
Disclosure: I have a new, never used GiPro in the classifieds for sale. I'm one of those tech geeks who is comfortable with reprogramming the ECU so I went that route (after ordering one).