A->B->C with 2 tickets, several hours of transfer, and for B I'll normally need a visa

(Note: I don't know the transfer process and policy at Jaipur airport, the visa checking policy of AirAsia, or whether the check-in for Air India Express can be done online. But I'm posting this answer because other answers incorrectly suggest that this would be sold as one ticket with one PNR.)

When you see "Transfer protected by Kiwi.com Guarantee" it means Kiwi is buying two separate tickets in your name, with two different passenger name records (PNRs). Therefore, the airlines won't help if, for example, you miss the connection due to a delayed flight. The good thing about the Kiwi.com Guarantee is that if a delayed flight makes you miss the connection, Kiwi themselves will (generally) find you another flight to your destination.

Depending on the airline, you may even have to exit security at the intermediate airport in order to check in with the second airline, then re-enter security.

Unfortunately for you, Kiwi won't help if you're denied boarding due to a visa issue. Kiwi's fine print says:

Kiwi.com is not responsible for any visa issue, including airport transit visas; this is the responsibility of the passenger. Kindly note that without the correct documents, you may not be allowed to board the aircraft. You can learn more about your visa requirements by visiting the IATA Travel Centre or by contacting the embassy or your foreign ministry.

However, in this case, how will kiwi ensure that I even will be allowed to board a plain in Thailand without having an Indian visa?

They don't. It is your responsibility as a passenger to have all required Visa and you agree to that during the booking by accepting the terms and conditions.

There'll be 2 different tickets, right?

Yes, it's two tickets. Otherwise it would say "Transfer protected by the airline".

What will I tell in Thailand "I won't leave the transit zone thus I don't need a visa?"

Since these are separate tickets, Air Asia will NOT allow you to board unless you have a valid Visa for India. As far as they are concerned they are flying you from DMK to JAI and that's it. They have no knowledge or control over what you do once you get to Jaipur, so they must assume you want to go into India.

You need to collect your bags and do a full new check in for the second flight. In many airports you need to leave the transit zone to do this. Often, after the baggage claim there is no way back to the transit zone and/or there are no check in counters or bag drops in the transit area.

One point that has surprisingly not been mentioned until now is that if you have two tickets (which I'm pretty sure will be the case here), you most probably won't be able to check your luggage through.

That means that if you have checked luggage, when landing in Jaipur, you'll need to go through immigration (entering India), get your bags, go through customs, go to check-in to drop your bags, go through immigration again (exiting India).

So I'm pretty sure you will need a visa. Not sure if there are special transit visas in India, though?

Kiwi doesn't care. AirAsia does, very much so. But if you buy this trip, it will probably be on one ticket, with one PNR. And even with two PNR, you'll still have proof that you don't plan to enter Jaipur, but fly onwards.

This will be enough for AirAsia to let you board their plane.

Your PS has not been answered yet:

As others have already said, this itinerary will most likely result in two different tickets. Assuming that Air Asia's policy is to let you board without a visa for India if you can prove that you are just transiting, then yes, you will also be allowed to board if you buy the two tickets yourself. From Air Asia's point of view, you have a ticket for them and an onward ticket for another airline, independent of whether you book through Kiwi or not.

So it really depends on Air Asia's willingness to let you board and also on whether it will be possible for you to stay in the international transit zone of Jaipur Airport (if such a zone even exists) for the entire layover.

If you read the kiwi booking page, it literally says self check-in and in addition warns you about the transit visa requirements. So there is no way you can make this flight unless you have a valid visa before you board the flight.

And Jaipur airport website says it has only one terminal common for both domestic and international flights. So there is no airside transit area available for you anyway.

So book an alternate route preferrably on a single ticket.