All of the above is true. As the Gelb article says, the Phllies have not been especially good at development for 140 years, with just a few outlier epochs.
And the Middleton era has still been very crony-like, including Gillick's influence. That is the main reason the Klentak era failed so spectacularly (both because MacPhail was a bad hire and because Klentak had the deck stacked against him as a baseball guy in addition to not being a skilled manager of employees, it seems).
It's also the main reason they stumbled into the good luck of hiring Dombrowski after nobody else (and nobody analytics-minded) wanted the job.
The teams that are really good at this - the Dodgers, the Braves, the Red Sox sometimes, the Yankees to some extent - already had a deep base of development and scouting success, to which they added analytics and money (except for the Braves, though they are also not small-budget). The Rays are probably the only team of the Moneyball era that have actually sustained success (but like Oakland, that still hasn't won them anything). Beyond that the various analytics family trees, including Friedman's and Beane's and the Astros, have been a mixed bag. The Dodgers are just lethal because they've got all three things always working.
Tampa has the benefit of both being forced to innovate (to save money) and having no cultural/organizational baggage. They made their own mold.
I still don't see things as completely dire, however. The team has been nothing but successful at the major league era and the lower levels of the system and some of the dev changes seem to be posiitive. The current ranking is still a combination of trades, graduation and bad luck, and the lack of impact guys at the highest levels until recently was still as much from the Klentak draft years. Barber's guys, at least in the first-round, only just arrived this year (and last year in Abel's case).