The general rule of thumb is that an alternator won't take the batteries much over 85% capacity. A shore charger will take them to 100%.
This is because the alternator's output voltage is designed such that you can motor for long periods without fear of overheating the batteries, which is good, but the downside is they only reach 85%.
So that's why your charge rate with the alternator was so low - you were already at capacity, as far as the alternator is concerned.
The shore charger is rather smarter, and switches between various modes.
This is not the case. Both shore chargers and alternators simply regulate voltage. That is all they do. The battery bank determins how much it will accept at a specific voltage. The battery bank has no idea what is charging it. A dumb regulator will actually charge to full faster than most "smart" chargers because it stays at absorption voltage indefinitely.
The reason the 85% number is used is not because of some magic inside the alts voltage regulator but because we as sailors won't & don't generally run the engine for 10+ hours at a time.
It is simple battery acceptance rates & voltage that determines the length of time it takes to get to "full" not the alt or shore charger. Shore chargers just have the luxury of more time to do what they do than an alternator on a sailboat. Run the engine long enough and you'll eventually get to .5% acceptance or less. An alt will most definitely get your banks full, if you give it the time. The only time an alt won't get a bank full is if the voltage regulator is set too low, like 13.6V or if the system has massive voltage drop problems. This of course has nothing to do with an alternators capability just that it is set wrong or the wiring is insufficient. A properly installed 100A alternator will charge as fast as a 100A shore charger if both have the same voltage set points.. (except when that alt gets hot it will run at 75-80A and the shore charger will often shut down on over temp if run at max for long enough)
We now have a LiFePO4 bank (Lithium Iron Phosphate) and just had to wire in an alternator regulator CUT-OFF switch because these batteries don't have the acceptance issues that LA batteries do... It is an ODD feeling to have to turn off your alternator because the bank went from 70% SOC to 100% in an hour......
Using that same exact alternator on my LA bank, in that that same scenario, took roughly 10+ hours to get to full from 70% SOC.......
Our alt can charge the LiFePO4 bank to full from 70% in about 1 hour. It took 10+/- hours with a lead acid bank using the same alternator... No changes other than programing the regulator for a lower charge voltage for the LiFePO4 bank... Lower voltages normally mean slower charging but not so much with the newer battery technologies....