I've found the opposite to be true, rarely have I see a 6 speed transmission where you have an "overdrive" 5th as well as an overdrive 6th. Unless it's something with an absurdly high top speed and a hell of a lot of horsepower. i.e. Lambos and the like.
Nearly all the BMW M series have 5th as the 1:1 with everything before it being closer together, rather than just adding potential higher top speed. Same with the higher powered subarus. Their 5th is close enough to 1:1 as makes no difference.
For a vehicle that tops out at around 115-120 or so, having a closer ratio transmission, while there's the possibility for a little more rowing, it gives you a lot more time in the sweet spot in your torque band and you don't have an absurd drop from 1st to 2nd.
Regarding autocross the less time you have to shift, the better off you are. I don't think that many of the M3W crew are doing autocross though.
I think for the Miata itself though skipping gears can also be attributed to what rear end you're running. What's the ratio yours is running?
I'm definitely with richard on this though. I love a close ratio 6 speed for overall driving, than a 5 speed with a lot wider spacing.
Both the 5spd and 6spd NC miatas run 4.10 rear end/final in the US. I do not know if a different read end/final is offered in other parts of the world.
For comparison sake NC ratios below;
5 Speed
1st-3.14
2nd-1.89
3rd-1.33
4th-1.00
5th-0.81
6 Speed
1st-3.82
2nd-2.26
3rd-1.64
4th-1.18
5th-1.00
6th-0.79
If you notice, the ratios are extremely close both in the low end and on the higher end which leads many to skip gears. While shifting in AutoX is due to the fact of not wanting to shift often, with such close gears it leads to almost no advantage to shifting and doesnt help much in keeping you in the ideal torque curve, but rather eeps you peddling through gears or skipping them on leisure drives. While this can be fun, I dont think it results in much of an advantage over the 5 speed.