Mahakam Ale is the preferred choice because it's more reliable. After all, it's faster and easier to maintain at least one unit on each row than it is to have six units total.
Petri's Philter does have a few minor advantages, but those are only good in certain situations.
1. It's less susceptible to Scorch.
2. You can row stack units, if you want.
3. Maybe the most important difference is that Petri's Philter works better with Mahakam Marauder.
4RM3D has summed it up pretty well. Basically, to get full value from PP, you need to have 6 units on the board. It is actually a very hard condition. You need a long round and plan very carefully and you can never be sure how long a round will go. With so much removal in the current meta, it is not guaranteed that you would get full value from PP. MA, to get the full usage is very easy and quick. Your third unit can tutor it go get full value.
But MA could give a very juicy Scorch or AC target with huge point cards on board for your opponent too. I haven't used both, but I would prefer MA over PP any day.