If a battery is completely flat there are 2 major considerations :
1. How long has it been flat ? If a lead-acid is left in an uncharged state for more than a few days the lead start to sulphate, this wrecks a battery PDQ. A "smart" charger that gives higher voltage pulses over a very short time can sometimes fix this, but it is often time to replace the battery
2. A car electrical system has no current control, only voltage control, usualy at around 14 v. The battery "state of charge" forms the resistance that limits the amperage that flows into a battery, the higher the charge, the higher the resistance, so the current flow is reduced. A very discharged battery has a very low internal resistance. This can lead to extremely high current flow through the charging circuit, hopefully fuses will protect the alternator from damage, but there is a risk. The high current flow through the battery can lead to overheating (boiling) of the acid, and/or distortion of the plates. If they touch an internal short forms and the cell dies. This is not recoverable.
For the above reasons it is preferable that a discharged battery is charged "off car" by a dedicated charger. These have internal controls that limit the maximum current to prevent (2), and "smart" chargers have a chance of fixing (1)
A 60 amp hour battery fully discharged will take about 20 hours at 3 amp rate to recharge. If you let the car charge it up in 2 hours .. you've stuck an average of 30 amps at it !!! The maths is quite simple. But what was the "starting" current flow ... probably much higher ??
HTH