I don't think that the UNIX certification even solved the original problem it was trying to solve in the first place. Apple binaries still can't run anywhere but on Apple. There's still little endian vs big endian encoding battles ...
I partly disagree.
Running binaries from one OS on another OS: That's somewhere between hard and outright impossible. Java got close, and for a while in the 90s simple Java programs could be shipped between machines. Recent experience has been that while Java code runs, real-world programs that solve real-world complexity problems are too dependent on environment to work.
Litte-endian versus big-endian: For many problem domains, this is a non-issue. For example you do database queries, retrieve the results in a high-level language (not C or C++), communicate with other programs either via text streams or using a good RPC package, and do other IO in text format, the issue doesn't even arise. For bit-banging code, if you write your code carefully, it can be dealt with. Experienced programmers have dealt with this so many times, it's getting boring. A slightly bigger problem is the 32 <-> 64 bit chasm, but again, we've learned how to deal with it.
I think Posix and SUS mostly solved a gigantic problem. I started programming on Unixes in the late 80s, where porting between BSD-style and SysV-style machines was annoying and tedious. A significant fraction of system calls were different. Beginning in the early 90s, the trick was simply to code to published Posix standards, and many of the problems went away. Not all, and for esoteric edges of the system call universe (like file byte range locking, async IO, signals) it was still not completely trivial, but 90% of the work of porting went away.
Now did certification solve these problems? Perhaps indirectly, by forcing Unix suppliers to actually become standards-conforming. But for the most part, they already conformed with 90% of the standards anyway. The same is true today: If you write C code with lots of system calls to Posix specifications, it will usually run on Linux and *BSD, even though neither is certified.