In general, 3D FEM has particlar stability criterion regardless of software.
Here is a nice summary for CFD from Flow Science (Flow 3D)
More generally -
Certainly mesh generation is important. I am not particularly familiar with GAMBIT, but I expect there is a default node/element density.
In certainly problems, the meshing would need adjustment, particular where there are large thermal gradients, otherwise the elements require appropriate shape/form functions. Computational efficiency is another issue that must be considered.
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