I have been living in Thailand now for about two years. It is a special place.
Either you love it or you hate it. Well... I hate it. Why?
Exactly the problem you bring up here. Every office and every official makes up his own rules and has his own policy. It does not matter what the written law is, even if you have the law book in your hand, they will smile and tell you: "yes, you are right, but our policy is..... bla bla bla..."
So, as a result every freight-forwarder is extra-careful and hesitant. They have no clue what is going on. Even offices inside Thailand have this attitude.
But the reality is:
If you enter Thailand with a motorbike (and the proper proof of ownership) you simply get a 'temporary import permit' (the white paper). It does not matter whether you come by air, by sea or by land.
If you try hard enough they will (in most cases) even use your carnet, but I would advice against it since it often couses problems when leaving the country.
I do have one word of caution though. This 'white paper' is only valid for one month. Even though the law is very clear and states that "the temporary import permit will be issued for the duration of your stay as long as you have a valid visa", the 'policy' of customs is: "only one month".
Since many travelers leave Thailand to visit Burma and to get an other 30-day stamp in their passport, this can create a major problem.
When you do this, you need to get a stamp on the white paper to. If not, you are in for a very expensive surprise when you leave Thailand with your bike.
For the rest I can only say: Thailand has many many nasty problems, but brining IN your motorbike by sea, air or land is NOT one of them.
Literally dozens of travelers fly in from Nepal or India every year. Non of them had ever a problem entering the country.
As I said in an other post: Even if you would want to pay import-duty's... You can NOT. It is simply ilegal to import a motor vehicle without prior permission from the ministry of trade. And when you get this permission you have to pay 300% duty. A law to protect local industry dictates that 60% of the vehicle must be manufactured inside Thailand. All those new Toyota's and Isuzu's you see driving around, they are all "made in Thailand".
I hope this makes things a bit more clear.