From at technological stand point:
The Normandy's primary cloaking technology is heat sinks that keep it from giving off broad/no EM fields in the infrared. That is however just a tiny sliver of the radiation that a starship would emit. You would have radio wave noise from just the flow of electricity to effects of the ship on space itself (gravity). Your would have to find a system that would cover all these effect, the "cloaking device" from Star Trek does that is a tidy package. The Normandy's suggested cloaking device just covers a tiny portion of the issues that need to be addressed.
So would it possible to building new systems that are not the "hand waving" solution presented by the canonical cloaking device? Sure. But we move on to other matters...
From a philosophical standpoint:
A goal of the Federation has been to foster peace in the galactic neighbourhood. Being closed off, sneaky in both governing and operations through the use of cloaking devices would not facilitate in achieving your goal. Though as noted in the comments there are exceptions, though I would consider tactical advantages from the environment while being hunted isn't wrong.
With nothing to particularly cite, I would motion that any explicit hiding of a ship's normal operational output would be considered cloaking and in violation of Treaty of Algeron regardless of what technology you use. However, any advancement, like Voyager's neural-gel packs, or light-based communication that decreases a ship's EM signature would not be cloaking.