Of the four disadvantages of PHP mentioned in the article, in my opinion, the worst by far is the first, i.e. confusing comparison rules. The article however fails to explain that clearly: the worst thing is not that comparison rules are just confusing (heck, many things are confusing at first, but eventually you work them out); the worst thing is that those rules are intransitive (!!!), as explained very well here: http://phpsadness.com/sad/52
The second disadvantage, passing by reference vs. by value, honestly can or cannot be confusing, depending on which other languages you are accustomed to. So I would say it is a debatable point.
The third point, the language being failure-adverse, is a choice made by design, this is also a debatable point, but it's in line with the fact that PHP was created as a utilitarian language as Lerdorf explained numerous times, e.g. here https://www.youtube.com/watch?v=anr7DQnMMs0
The last point, inconsistencies in the standard library, is obviously true but I would say it is very common in languages that have been around long enough to have subsequent approaches layered in the standard library. Some languages resolve this by making breaking changes and keeping consistency (think Python 2 vs Python 3), some others just show their age by having libraries that were developed at different point in time (Perl, R and Java come to mind), this is also explained by Lerdorf in the video linked above.
The second disadvantage, passing by reference vs. by value, honestly can or cannot be confusing, depending on which other languages you are accustomed to. So I would say it is a debatable point.
The third point, the language being failure-adverse, is a choice made by design, this is also a debatable point, but it's in line with the fact that PHP was created as a utilitarian language as Lerdorf explained numerous times, e.g. here https://www.youtube.com/watch?v=anr7DQnMMs0
The last point, inconsistencies in the standard library, is obviously true but I would say it is very common in languages that have been around long enough to have subsequent approaches layered in the standard library. Some languages resolve this by making breaking changes and keeping consistency (think Python 2 vs Python 3), some others just show their age by having libraries that were developed at different point in time (Perl, R and Java come to mind), this is also explained by Lerdorf in the video linked above.