The semi combustible 125mm propellent stubs are the problem... externally they are cardboard with a metal stub case, the core problem is that if you have the propellent stubs sitting vertically in an autoloader on the floor of the turret, then any turret penetration that leads to showers of sparks and burning hot bits of metal entering the turret will lead very rapidly to those propellent stubs catching fire and with them all stacked together if one goes then they all go in rapid succession.
The western 120mm rounds at least have a metal case around the propellent which protects it from sparks and embers.
The T-72/90 arrangement with the propellent stubs lying down reduces the horizontal area that a penetration could hit and reach the propellent stubs, but the arrangement of protection plate over the ammo in the autoloader prevents sparks from reaching the highly vulnerable propellent stubs, and of course the APFSDS rounds that are also lumps of propellent and sabot.
A design solution is to simply separate the ammo and fuel from the crew compartment in design terms, which is T-14 and the T-14 equivalent to the Boomerang and Kurganets vehicles, the short term solution for other vehicles is to not carry loose ammo in the crew compartment, and only under the sheet metal protected autoloader or other protected areas (ie in T-90 the turret bustle container and a small ammo container between the engine and the turret bustle).
Longer term I would think liquid propellent guns with a binary or even more separate propellent components that are stored separately in the vehicle and not mixed till they are put into the chamber would be the best solution for a chemical energy gun, while EM guns would remove the problems completely if they can be made to reach the necessary level of performance.
Of course no arrangement of ammo and fuel will ever make tanks safe on a battlefield... mines and drones and missiles and artillery and other tanks will always be a threat and thinking fixing this or that will make your tank invincible is just childish.