You couldn't mount them, but you could build the towers and such. Which... you know... is kinda how it would have to have been.
Hrm... what's the best way to explain this.
Think of it this way. Imagine the lord of a castle. He just built a wall for the cheapest cost. It's a basic wall that as wall-y as can be. No special options, it has some fortifications and that's it. In Total War terms, this is what you're doing when you buy the regular walls. Then he poses the question to his Royal Architect... "hey nerdface, I want to put my sweet ballista that I collected on my campaign on my sweet new walls yo. Make it happen, douchenozzle." To do this, the Royal Architect has to bill the Royal Coffers again for a wall expansion to house enough room to put the ballistas, as well as make arrangements for easy transport of ammunition, etc. So this is what you pay for when you buy the towers. In this case the Royal Architect also bought an entire new set of ballista as well because he's collecting bribes from private contractors.
IRL you wouldn't have been able to just randomly mount catapults or cannons without building infrastructure to house them. That is of course what the in-game systems were designed to simulate. These things don't come out of thin air. In fact I'd say the Total War system was unrealistic not because you couldn't integrate the siege engines into your walls at whim... but because you couldn't TAKE OUT the siege engines you built into your fortresses.