The gravity suit made its debut in Super Metroid where its purpose was to nullify the effects of viscosity and cut damage by a quarter. During game play, the player would learn that the gravity suit would prevent damage from the effects of conduction from magma. It was in Metroid Prime that the gravity suit was affected by magma and lava, making some fans think this was the result of a game mechanic or the magma and lava were superheated. I suspect the latter was the result of the description of the magmaul found in Metroid Prime Hunters, which uses “superheated magma” in its description.
The alternative could simply be that there are different types of gravity suits, all with the same name. Aqua pirates, for example, are known for using gravity suit technology. The gravity boost—a creation of the Luminoth—likely uses gravity suit technology as well. The purpose of the gravity suit is mainly to nullify the effects of viscosity and gravity by normalizing it in a way as if Samus was walking outside of water and experiencing the gravitational acceleration of 9.81 m/s^2, even under extreme gravity. The negation of the temperatures of magma is simply an unnecessary addition.
If anything, the varia suit would be better off negating extreme temperatures from conduction for the simple fact that its name is from the Japanese, which would literally be “barrier suit”. “Barrier” can be used for anything that’s meant to either withstand or reduce the damaging effects of energies, forces, temperatures, electrical currents, optics, &c. Anyway, it is typically assumed that the gravity suit prevents Samus from receiving damage from temperatures under 700°C. Temperatures greater than this explain why the gravity suit doesn’t protect Samus from the magma and lava in Metroid Prime and Metroid: Other M.
My take on this is the gravity suit in Metroid Prime is different from the gravity suit in Super Metroid and Metroid: Other M because the damage reduction in Metroid Prime is 20%, but 25% in both Super Metroid and Metroid: Other M. Since the time between Super Metroid and Metroid: Other M aren’t far off from each other, and since most of the same upgrades show up in the latter that were present in the former, I see no reason to consider the gravity suit in both to be different from one another, save the name of the suit itself.
To determine what possible lava type we’re dealing with in Metroid: Other M, we’ll need to examine Sector 3/Pyrosphere. After all, it is this game where the inconsistency between it and Super Metroid begin. Indeed, some have wondered what the liquid is in the depths of Norfair. While it looks more like acid, it’s probably supposed to be magma. Magdollites dwell in lava and lava adheres to their body. They also cannot go outside of lava.  So it would follow that the liquid that looks like acid is actually a hotter type of magma.
This would make what seemed inconsistent no longer the case. In Sector 3/Pyrosphere, Samus encounters an active volcano. This volcano takes the shape of a stratovolcano. According to San Diego State University’s Department of Geological Sciences, “Andesite commonly erupts from stratovolcanoes, where they form small-volume flows that typically advance only short distances down the flanks of a volcano.”  We know that the lava flows in Sector 3/Pyrosphere cover at least several kilometers.
Possible reasons why the sector is covering several kilometers may be due to Goyagma’s activity in the volcano. The volcano in the sector can be seen two rooms from where Samus defeats an asborean. As Samus heads upward in the volcano, the lava begins to rise, leading to the battle against Goyagma. It’s after defeating this boss that the lava recedes and the volcanic activity ceases. Or it could be that the sector was constructed this way. Or it’s possible that this volcano’s lava type is basaltic. However, while rare, it is possible for andestic lava to cover 8 kilometers. 
Whatever the reason, I think it’s safe to work at least with the andesitic type, simply because this is the common type from stratovolcanoes. With this in mind, I can look for the temperature of andesitic lava. From the looks of it, the temperature can range anywhere between 800 to 1,000°C.  On a low-end, this means Samus can resist heat below 800°C.