Ah, but transparent huge pages are portable. They don't change your code. In HPC land, your task pretty much own the node(s) on which you're running, so there is little danger of the fragmentation you encountered. THP often is a big performance win with *no* code change. Fixing the zero page issue will fix the remaining decently-sized gotcha for HPC-style uses.
And some of these HPC codes are old and/or expect to run on more than Linux. Conditionally changing all the user-specified and compiler-generated memory allocations is a painful task.