The GI-Pro does fool the ECU into thinking it is higher gear, and making those tables for ignition available all of the time. Just like a TRE (timing retard eliminator).
I use a dyno and exhaust 5 gas analyzer (rarely just a Lambda sensor), but yes, you really need some way to measure what you are doing - fuel, ignition, and output.
Running 91/93 PON
US/98 RON
EU fuel, the R3 tends to want a good bit of timing at lower rpm and loads. How much depends on the bike and a few other things - engine and air temp, coolant, cylinder demands, etc. Too much advance and you get occasional preignition and burst knock, and output drops.
With you being in northern Europe, you have very good/consistant fuel, and low ambient temps. Output will tend to drop before irregular combustion sets in.
If you are running a canned map with little of no additional advance, making all ignition tables the same is not likely to hurt anything. It is when you get bad fuel, or start changing maps that already have additional advance, that you can get into trouble.
You can't run a lot of ignition advance when lean. This can be an issue on bikes that have injectors that do not flow well at low engine speeds (low injector open time/IJPU).
Generally speaking, many R3s need more fuel in cylinder 3. Not all, but many.
Get the fueling correct first, then test ignition advance.
Watch ignition advance changes with a Lambda meter (wideband O2). You will see changes in Lambda/AFR when you only make changes to ignition advance... one of the drawbacks to LSU/UEGO sensors and the way they read residual O2 in the exhaust.
And realize that making the engine too responsive in 1st gear, can make the bike hard to ride aggressively.