You and Exdraken have already pointed out a lot of factors that are germane. Another significant one is the technical capability of the pods under discussion. Just like aircraft, they're designed for a particular set of tasks, and therefore have limits on their capabilities. No ECM pod magically protects any aircraft from all threats. Earlier generation pods in particular were usually designed to address very specific threats. Some level of programmability to adapt to different threats was eventually developed as the technology improved. Later generation pods are truly flexible, but again will never cover every threat out there.
Chaff and flares seem simpler, but when/how/where they're deployed can be as complex as ECM pod use. Old tactics and systems will generally dump a lot out when you hit the button, new ones will sequence them out at a specific rate under specific circumstances.
Equipment standardization between allied air forces of course only goes so far. National "variety" in EW gear (just like aircraft types) will occur. It may reflect a different tactical philosophy (stand-off at high altitude vs low level), or a host of other factors. ECM isn't total protection, it really just buys time. So a fast low level striker may need just a little time. Of course there are other threats at low level, so it's a choice.
You're correct to intuit that ECM always incurs a penalty (weight, complexity, pylon station), so it's best to only include enough on board to do the job. Off board assets available (EA-6B, EF-111, EA-18G) will also contribute to survivability. And stealth of course reduces the overall need for ECM, and also improves the effectiveness of ECM available.
TLDR: different pods do different (classified) things, and it's a compromise!