I'm sure HST's have similar capacity to a Pendolino, yet far more seats line up with the windows.
Oh come on - you must be being deliberately obtuse.
The bottom line of the problem is not enough seats have window views in the 390. Why? Because the window pillars are very thick. Why? Because of their design, and their construction...
Each window pillar hides a vertical support stanchion, which pretty much goes the entire height of the car. It is physically impossible to make the windows any bigger on the design. You could make them bigger and redesign them if you a) lessened the tilt to 6 degrees like the Voyager, but you'd lose time or b) removed the need to tilt all together, but that won't work.
The windows can't be any higher due to the body profile required for the 9 degrees tilt. The cylindrical design of the body is designed to be safe, as safe as possible. The windows fit perfectly where they do as if they went any further round the body, they'd be subject to stress in the event of any impact and fail.
In short it's a trade-off. The design of the train makes it as fast as possible, it tilts at 9 degrees with a lot of 125mph running. If you change the design in any way, it'll suddenly become less good at its job.
Wrt to slotting luggage racks in pillars etc, you'll just lose seats! The Pendo has a high capacity, lessen it and you'll get more disgruntled passengers. The basic design of the tri-ribbed carriage results in three equal sized bays (best seen in coach E) where between each internal pillar stanchion (6 per car, 3 down each side) you have 3 windows between each one; 1) a table at the first window (4 seats); 2) 2 viewless pillar seats behind; 3) 2 very good view airline in the middle of the second window; 4) 2 not so good view behind through the second window; 5) 2 behind looking straight side through the third window; 6) 2 behind looking forward through the third window.
That's 16 per side per section, that's 32 per section. 3 sections results in 96 per car before we start messing around with luggage racks, disabled seating and priority seating. Every time you take seats 2) out (the worst seats on the unit) you lose 2 seats every time, and you can't satisfactorily replace them anywhere.