The problem would be that the reservation system does not take into account the fact that passengers may want to make their connections by being at the gate at the stated boarding tme.
If the actual boarding time is moved up (compared to the stated 'official' boarding time), then the reservation system will have no way of guaranteeing that PAX can arrive at the boarding gate for tight connections prior to boarding.
Some FF's mitigate tight connection issues by avoiding them. However, the odds are that if one books for an earlier flight, there is less chance of being stranded overnight, especially if a reasonable connection time results in booking for the last flight.
Just guessing, but early boarding might be a policy to try and avoid the snowball effect of one late flight, at least until later in the day.