If Pennel got suspended because of using marijuana he was already caught for the fourth time since entering the league. The Journal Sentinel mentioned in an article that the four game suspension indicates it was for a harsher drug. It's possible they know that he hasn't previously be fined by the league.
While I got the sequence wrong, the JS article did not say what you said. The article is also misleading in its incompleteness.
In the absence of procedural violations, an alcohol issue or a behavioral issue, you are correct that 2nd. and 3rd. violations for pot result in only fines, with a 4 game suspension at the 4th. violation.
What neither you nor the JS article said is that for non-performance enhancing drugs other than pot, the 4 game suspension comes with a 3rd. violation.
The mere fact of a 4 game suspension is not compelling one way or the other.
Now, I'm sure hints and rumors about who uses what and when swirl around the clubhouse and front office. If the JS writer got a whiff of something and means to provide a hint, that's anybody's guess.
I find it a reasonable conjecture, as I said before, though not a certainty which I did not suggest, that the issue is pot because of the reported prevalence of it's usage.
There is a another consideration as well. Though the science is not precise, for a heavy pot user THC could take as long as 3 months to pass a urine test. For codeine, to take one example, it could be just a few days to clear in a urine test. I don't see anything indicating the NFL uses anything but urine tests. In other words, a pot user is more likely to be caught than users of other drugs.
Of course getting arrested (as in the cases of Jones, Guion or Jolly) is a different situation going to the policy of "conduct unbecoming".