Well, you are partly right. I don't believe they can easily have windows in a bombproof chamber, though it's not out of the question that this might be developed, though no doubt at some cost in weight.

However, if you leave out the bombproof concept, windows are not a problem, there are just 2 of them. Strictly speaking, the passenger module could actually be open on the sides, other than the risk of passengers catching things or hurting themselves as the module slides out of the train and into the empty aircraft hull. So it could either have thin regular windows set to align with the pressurized windows of the hull, or it could have panels that slide up to protect you while things are moving, but open up to see out.

Windows actually do perform a role. Looking out the window is the best protection against airsickness.

If the passenger cabin is pressurized, the outer hull could have more ordinary windows as it would not be.

Now in this case a bomb would blow out the windows and depressurize the plane. This is not the end of the world of course, as oxygen masks come down and the pilots would not be affected, and the plane would descend quickly.

The real issue is making sure that a bomb doesn't make the aircraft unairworthy, and thus kill those who were not close to it. That's the difference between bombs on trains and on planes, a bomb on a plane has a better shot of crashing the plane and killing everybody else. I'm not skilled enough in the new bomb-resistant designs to know if they could handle windows that blow out. (Blowouts forward of the air intakes could also present a problem.)

It is actually much harder to blow out an airplane window than people think, as Mythbusters discovered.

Key to this design is modern fly-by-wire. With fly-by-wire, aircraft control goes over multiple redundant data cables. You can sever most of them and not hurt control. Slightly more expensive is to have enough redundant power cables so severing those will not disable the aircraft.

Right now the key is that it's much easier to scan for and prevent big bombs, so the thing that needs heavy passenger/bag scrutiny is small bombs. If you design your plane so that it can survive small bombs, you don't need that heavy security, other than to protect the passengers who will be near the small bomb. Which of course you would like to do, but in reality you can't prevent suicide terrorists from finding closely packed people and blowing themselves up among them. Stopping it in the skies is of no special extra value compared to stopping it in malls, on trains, and in airport security lines -- which are inherently unsecured and could be subject to large bombs. If you make the situation similar to a train you can have similar security needs to rail.