There is an interesting history to covert channel analysis and modern side channels. It wasn't until the late 1990s (as far as I can tell) that anyone made the leap from covert channels --- which have cooperating agents on either end of the channel --- to side channels, in which the transmitter is unwitting.
It's possible that there's other interesting side channel stuff lurking in covert channel analyses. But I think the research link there is also pretty well known.
At any rate, what this analysis primarily concerns itself with is the suitability of x86 for multiuser multi-level security (MLS), in which you have differing levels of classification and absolute barriers to sharing information between those levels. In that setting, a covert channel is a serious problem (it allows you to bypass the MLS barrier). But in modern industry computing we've largely moved away from the concept. You can think of this paper as referring to a different concept of "security" than the one we think about.
Except in cloud computing, where multiple and mutually untrusted users are sharing the same hardware... and that's where the side channels are the most concern. If Meltdown/Spectre were discovered 10 or 15 years ago, when cloud computing hadn't quite grown to what it is today, it would probably have received much less attention.
In the public domain, anyway. Presumably NSA folks had thought about this in the context of TEMPEST-style attacks?
Unfortunately, this hardware cannot safely be dismissed as "simple" or not in need of in-depth analysis. A relatively simple interface can hide vast implementation complexities and the 80x86 interface is far from simple. For example, the Pentium contains approximately 3.1 million transistors. Its instruction processing and pipeline architecture are extremely complex.
Now we have billions of transistors in a single chip.