If the object is stationary in the scale's frame of reference, it's simply mass (not relativistic mass) which increases.

The object is stationary relative to scale's frame.

The atoms making up the whole object can move due to thermal motion.

If the object (centre of mass) is stationary with respect to the scale's frame, it doesn't matter if the atoms inside move or not: any increase in the object's energy will be measured as an increase in its mass (the one you call "rest" mass but it's simply called "mass"; if you want to compare it to relativistic mass, I prefer the term "invariant mass" instead of "rest mass", because, for example, photons don't have any frame of reference in which they are "at rest", but they however have an invariant mass).

Will the scale indicate the same value at 200K and at 900K ?

No, as I wrote, the scale will indicate a greater mass at 900 K

the system's mass, however, *is not* the sum of the masses of the particles (mass is not additive).

This is counter-intuitive and I have 2 more questions:

1) rest masses are additive?

I wrote it. It's *not* additive.

2) is there a simple intuitive reason why masses are not additive?

Example: you have an electron and a proton in a stationary hydrogen atom at the fundamental level. You measure the atom's mass and you find the value M

_{a}. Then you separate the electron from the proton, you measure the electron's mass when it's at rest and you find the value m

_{e}, the same with the proton and you find M

_{p}, but M

_{a} is not equal to M

_{p} + m

_{e}, because in the atom there is also the binding energy (in this context it's not important if this binding energy is positive or negative).

The total mass of the atom M

_{a} is its total energy E

_{a} divided c

^{2}: M

_{a} = E

_{a}/c

^{2}, but in the compute of its total energy E

_{a} there are *not only* the rest energies of the masses m

_{e} and M

_{p}, there also is the binding energy.

Every time two particles (or bodies, or objects) A and B can form a bound state AB, the mass of the system AB is not equal to mass(A) + mass(B).

In chemistry these differences are actually very small and irrelevant; in nuclear and subatomic physics, not, because the binding energies are greater.

What is additive is

energy.