I can't seem to understand the difference between these two terms.
A simple answer would be that the controllability of an aircraft is good if you can easily make it do what you want – ie go to and hold the bank angle you want, or ditto the pitch attitude or recover quickly and easily back to what you were doing before a gust induced upset and so on. It has nothing to do with the range of manoeuvres that the aircraft can (or cannot) perform.
On the other hand the manoeuvrability of an aircraft is good if it call pull a lot of g at a slow speed (they can all do it at high speed) and also has a high max roll rate. This combination enables it to carry out a wide range of manoeuvres.
As to your Q1 this 'reduced manoeuvarabilty' is not just a 'big-jet' issue. It applies to any aircraft that can go high enough to get a big split between IAS and TAS. At 40k as you know TAS is double your IAS. Lift depends on IAS while TAS determines the momentum, inertia and energy terms. So if you have (at sea level) 250kts worth of lift you can fight the 250 kts worth of momentum quite well and get the thing to manoeuvre. But when you still have only 250 kts worth of lift to play with but 500 kts worth of momentum (at 40k) then the thing appears very reluctant to change direction compared to sea level. It therefore feels (and is) less manoeuvrable.
On top of this going to high altitude will increase the Mach Number for a given IAS. Above about .4M aero efficiency starts to decline and by .8M it seriously reduces the amount of lift available from a given IAS and so makes the IAS/TAS thing even worse.
If you are with me so far you may well be able to answer your own Q2.
If not just say.