Help with smoke and liquid simulation in Mantaflow Original Post
This is the problem that led me to post this.
Whenever I scale the domain of a smoke simulation, the inflow object's smoke also scales up/down. Applying the scale of the domain does not fix the behavior.
Here's an image:

Notice how large the smoke boundary is.
Here's a video of what's happening:
https://streamable.com/3akto7
More issues I've encountered with Mantaflow:

When you set the cache method to &quot;Replay&quot;, the simulation won't bake when pressing play, like it should. Sometimes, if you manually drag the current time marker to frame 1 and then 0, and then press play, it will bake. This was a nightmare so I almost always use a Modular Cache as it seems more reliable.
If you scale the domain arbitrarily, it can mess up the entire simulation. Smoke or liquid will flow influenced by the new size of the domain, rather than the exact size of the inflow object. Applying the scale on your inflow object and domain does not fix the issue. The only solution I've found is to recreate the simulation entirely.
Collision objects don't work properly despite being set up correctly. For some reason I have yet to identify, sometimes collision objects will just get completely ignored by the simulation. No collision happens at all, and you have to recreate them, hoping it will work. Sometimes, it will work, but liquid will &quot;leak&quot; through solid collision objects.
These are mostly cache refreshing problems, but for now there are workarounds:

What you said. Bake the simulation manually. I usually use &quot;all&quot; since I still don't understand the types.
In the case of an outdated cache, change something like the &quot;resolution&quot; factor then change it back to force the cache to reload.
This seems to be limitations of the engine. don't make fluid move as fast, increase substeps, etc.