Shaos Zmaniyos... or not?

In this previous post I discussed the issue of Shaos Zmaniyos. This concept is usually taken for granted... but should it be??

Here is an excerpt from an interesting post (linked above) that I found from RYGB:

We are accustomed to assuming that hours of the day, for purposes of Halacha are relative hours (sha'os zemanios) — viz., the day is divided into twelve equal parts, from dawn to dusk according to the Magen Avraham, and from sunrise to sunset according to the Gra and Baal HaTanya. Hence, a sha'ah zemanis in Chicago today, according to the Gra is 0:46:55 hours.
It ain't necessarily so.
In the first place, the Pnei Yehoshua in the Kunteres Acharon to Berachos goes so far as to say that sha'os zemanios were an invention of the Rambam!
Secondly, the Meshech Chochmah (Bamidbar 25:23) derives that the Halachic hours of the day are standard, 60 minute hours (sha'os shavos) from our Gemara etc.