A spell says if limits to its casting exist

A creature can cast flame strike and ice storm indoors as easily as he can cast fireball and cone of cold.

You can compare this to call lighting, which says specifically

This spell functions indoors or underground but not underwater.

The areas make the spells different

The difference between the ice storm and flame strike spells and a simple fireball or cone of cold is their areas. The strike and storm are cylinders, which is a different kind of area than the more common cones and bursts. If you cast a spell with an area of a cylinder

you select the spell's point of origin. This point is the center of a horizontal circle, and the spell shoots down from the circle, filling a cylinder. A cylinder-shaped spell ignores any obstructions within its area.

So you can totally pick the roof over your head or a point in space 5 ft. above the target area.

The rules would have it do so, yes

The sorcerer’s elemental bloodline literally does nothing but swap the damage type of the spell; all other effects remain the same. In effect, an acid burning hands still launches a jet of flame and still sets things on fire – it’s just that the fire and flame now deal acid damage instead of fire damage. This can, of course, be easily justified as, “hey, it’s magic.”

Of course, seeing as acid’s effect is frequently described as a burning sort of feeling, this isn’t much of a stretch – the action to “put out the fire” could be “wiping the acid off” and “dousing” it could be “diluting” it. In most cases, “being on fire” is entirely equivalent to just “taking damage-over-time that you can use an action to end.” But then if you consider a spell that magically puts out fires – which would work – it gets a little tougher to explain.

It doesn’t have to be this way, of course. The DM certainly has purview to change something like this, and there is certainly room for adding variety this way. The problem is that the game does not define obvious substitutions to use; fire damage sets things on fire, but it’s less clear what the rest should do if you want them to all be distinct. Even setting up distinct damage-over-time effects is awkward – some spells douse fires, but there won’t be any spells that end these new damage-over-time effects that you make up.

Which is, of course, why the rules don’t do this: having a unique status effect tied to each energy damage type requires having the rest of the game react to that fact. Pathfinder doesn’t, and adding it now would be very difficult.¹ It’s much easier to say “it’s acid-damage-dealing fire, deal with it; magic, yo,” than to write out specific versions for each element, and then make sure they’re all reasonably competitive with one another, and that the rest of the product line takes into account, and so on.

1. ^{Remember, even when the elemental bloodline was written, much of “Pathfinder” was already “written” – the core rules did not change that much from 3.5, and most of 3.5 was just used as-is. A change like this would have required rewriting substantial portions of 3.5 that they chose to leave alone, and thus even at the “beginning” would have been very difficult.}