Arduino 16 MHz with only 3.3V?
Officially, no.  Practically, often but not always.


  If I follow the datasheet to the the letter, this configuration should not work. BUT... After some test, it did work.


The data sheet does not say that it "should not" work, it says that it is that the part is not qualified for operation at 16 MHz below some voltage higher than you want to use.  That does not mean that a given chip cannot work there, it only means that a chip that fails to may not be considered "bad".  Failure may be total and obvious or subtle.

In practice I have seen it work, both on small modified import boards and those with switchable power supply voltage.  But I also recall seeing it fail to work.

Two factors that can make a theoretical difference are part-to-part manufacturing variation and operating temperature.

Note that with an ISP setup you can change the fuses to run the chip on what was sold as a 5v external crystal board, to operate from the internal 8 MHz oscillator instead, and you can do this even while leaving the crystal on the board.  If you also change the brownout detector fuse, you can lower the voltage further, for example to operate without a regulator directly on two AA cells.  Of course that applies to the ATmega itself - any other active components on the board would have to be qualified for the intended voltage too.