I've done some tests on this ...
and I get different results to you....
Using a table of 1,000,000 rows with no indexes and
adding 2 columns at once took about 4s
adding 2 columns with 2 commands took about 7s
So better to do it in one command
Using a table of 1,000,000 rows with a single index and
adding 2 columns at once took about 9s
adding 2 columns with 2 commands took about 15s (8s + 7s)
Still better as one command
(Note : lots of rounding in these )
If the data is flushed out of cache then the times increase by 50%.
Adding 2 columns with 2 commands took about 21s (14s + 8s)
The first alter table gets everything off disk and the second doesn't touch the disk so much faster.
I suspect you will see the same effect.
BTW, I also ran this on a 35m row table with 1 index and it took 9 minutes which is substantially faster than your run. What hardware are you using ? What disks are you using ?