In real-life, one way to heel-and-toe (assuming clutch/brake/accelerator pedal order) is to slide your brake foot over so you can depress the accelerator with the outside of your foot (the part just behind your little toe).
As far as the tranny trick goes. If it works, it basically suggests that auto-set is not done properly. I would think you want to adjust first gear (effective first gear, ie. multiplied by final drive) to be low enough, and top gear to be high enough, and spread the others out in between so that shifting is smooth. That's what you'd expect "auto-set" to do for you.
But I guess in practice you're better to keep the box ratios assigned in the lowest-possible auto set, and then raise, by increasing final drive, effective first as well as effective top (as well as all in between) when attempting to go for a higher top speed. In theory that should cause you to have difficulty getting going from stop in first gear, but I guess in practice that doesn't matter.
Assuming the trick isn't really a trick--that is, the game isn't actually doing anything "wrong" in its gear calculations--I would think a refinement might be to always move individual gears to the right, closer to top, after a setting? That would raise first, but compress the distance between the other gears, perhaps making for better acceleration at high speeds. There's a shape to the curve formed by the bottom of all the shown lines which tends to be optimal.
If the game recalculated other gears when you changed final drive, that would be really annoying. (E.g. for people trying to replicate real-life gearing). What is vague, of course, is how the ranges for each gear are changed, and why they are restricted at all (except that ratios should progress properly; 2nd should always be a higher gear than first (a lower number), etc.). (On the other hand, to be realistic, your gearing should be restricted by feasibility of cog combinations required). Even in [size=+1]GT4[/size], however, one wonders how realistic at all the power curves are, beyond approximating peak torque at rpms and peak power at rpms.
Oh, for [size=+1]GT1[/size], and its calibrated gear charts.
But the torque curves in [size=+1]GT1[/size] were noticeably exaggerated. (Often torque dropped off so sharply that peak torque and power were given at the same rpm--something that doesn't happen in real life). That helps allow proper feedback for using MT in the game, I think. With a more realistic torque curve, the signs of over-revving wouldn't occur so soon or be so obvious.
(In [size=+1]GT1[/size] it was very important to keep effective first gear (first gear times final drive) low enough ( a big enough number--that product is actually the number of engine revolutions required to produce one wheel revolution) for many turbo cars, because turbo-lag was modelled in an extremely exaggerated fashion. If you thought you might spin out, accelerating from stop became an issue (though the handbrake helped, since it would cause the model to declutch, reliably for FR and MR, less so for drive trains with front wheels powered, allowing you to "pop" the clutch for a burst start). )