An indirect answer is to use the forms in MLS. We (the Stake Executive Secretary and me (Stake Clerk)) recently tried the online bishop recommendation form in the Leader Portal, but had to add a lot of information manually that is automatically filled in in the MLS form. From our perspective, using MLS is an easier choice.
I found it interesting that only the Stake President and Executive Secretary had access to the recommendation forms (per the access matrix) though I have access to the same forms in MLS.
Since you have to print the online forms out to sign, date and mail them (maybe this will change in the future) just like MLS, the only advantage I can see is for a president that lives a great distance from the stake center.
I'm not saying this is bad, options are always nice.
As for your specific problem, there are lots of "funny" things going on all over LDS.org these days. For awhile this afternoon, when I tried to get to LDS.org, the Classic Web site came up. It was back to normal this evening. So, maybe your president's experience was one of those temporary glitches that are often reported here on the Forum.
JLR