Mauro,
You already know the answer. If you need to tie specific supply elements to specific requirement element throughout the entire order-to-cash business cycle, you must use MTO; or one of the other scenarios that has individual planning segments (ATO, ETO, etc). That is the 'Best Practice'.
You are instead trying to torture MTS into behaving somewhat like MakeToOrder. The 'Best Practice' is....don't do it.
You can alter your availability checks to minimize such problems, but they never completely go away under MTS using standard solutions. MTS is dynamic, and the pegging of supplies to demands changes from minute to minute.
Some companies also run mass ATP transactions (V_V2/COMAC) to re-order the confirmations, so as to better meet their Business requirements. Such re-ordering typically cannot meet all business requirements under all scenarios.
These are the standard solutions. I am not going to suggest which changes you should make, because for every change I could suggest, you will counter-suggest a limitation/drawback.
Best Regards & Good Luck,
DB49