The most efficient way is with a directly connected generator and this generator would need to be compatible with battery charging requirements. I couldn't see you finding such a thing commercially suitable for use at 48v.

"The alternator's output is stepped down using an iron-core AC Transformer, then run through a rectifier to output DC current to charge batteries."

That answers your own question, that is not direct connection, you have included a battery charger even if simple and home built. Once you go the battery charger route then your original question goes out the window. The new issue is what is the most efficient battery charger.

Beyond this the issue comes down to so many factors that I can't be bothered to wade through it. The high tech battery chargers are primarily designed for mains use and their main purpose is to look after the batteries. On mains they take what is needed to do it.

Running these things from generators alters the equation where you are looking at fuel economy load etc and in most cases they are expensive and far from ideal but they do give ideal charging characteristics.

Your transformer and rectifier if using a suitable transformer will be as good as the expensive high tech things but will not be as good as a direct 3 phase alternator rectified and set up for battery charging directly at 48v.

Single phase is dreadful for battery charging.

You will have so much advice that you will be no wiser in the end.