In older versions, it is faster to just load the data into the table. Adding the indexes rebuilds the entire table via something like insert/select, so you might as well just do it once by inserting the data and building the indexes the first time.
In Plugin versions, it is much faster to insert the data and then add the indexes, because of its ability to add indexes online.
The parameters have a lot to do with speed. As soon as the index doesn’t fit in the buffer pool, performance drops very sharply.