Hello Sylvain,
The central repository is possible with most CAD system including Eagle. It's just a matter of discipline and proper archiving.
That is dangerous. Suppose you need a BC847 in a really small footprint, minimized to cram a lot onto a square inch of space in low power applications. Then you would use a BAT54 in switcher apps but want a larger footprint to squeeze out a little more thermal conduct, requiring a larger foot print. Both are SOT23 but now you would compromise one of them.
Regards, Joerg