@TrippyLighting
Regarding the two different results: this is related to surface knot vectors, a property of NURBS that T-Splines makes use of (and something you won't see in standard SubD modelling). I gave another overview of this concept here, in explaining how this relates to error T-points. Here's a brief summary:
The shape of a T-Splines surface is not only affected by the position of the control points - there are also hidden "knot vectors" embedded in the T-Splines body (something like a 'weighting' applied to edges on the model), which also influence the smooth body shape. You'll have seperate knot vectors in the 'u' and 'v' directions of a surface. You can think of the knot vector in one direction as a list of spacings between adjacent edges; something like this:

When you first create a primitive (like the above), all knot spacings will be equal to 1 (= 'uniform' knot spacing).
A fundamental rule to these knot spacings is that adjacent spacings (i.e. the spacing on opposite sides of each T-Splines face) need to match-up. You can't have one edge on a face be a '1' and the opposite edge of that face be a '0.5' or a '1.1'.
When you start inserting edges, in order for the numbers to add up, we need to divide the existing knot spacing values. Here's what it will look like if you insert a single edge:

(and likewise, deleting an edge would introduce knot spacings of length 2).
The ability of T-Splines to divide knot spacings like this is important in allowing things like T-points, 'Exact' subdivision, etc.. But the downside is that, as you insert and delete topology, the knot spacings will become de-regularised, and in some cases may lead to unexpected shape problems (if you have star points that looked screwed-up, or inexplicably large distances between box mode control points and their smooth mode equivalents, it may well be down to irregular knot spacings in those areas).
So this is why we have the Make Uniform command: what this does is try to reset as many of the knot values as possible to 1.
In your examples; the box created with 2x4 to start with has uniform spacing (1s all over). The 2x2 box starts with uniform spacing as well, but when you insert edge loops it divides these up and introduces some spacing of <1 (probably ~0.5 on your example). If you perform Make Uniform on this model, is should reset all of the knot spacings back to 1, and give you the same shape as if you had originally created it with a 2x4 box:

We don't explicitly 'expose' knot spacings because it's a fairly complex concept, and for the most part it's not something you need to be concious of - T-Splines are designed to take care of knot spacings in a way that make modeling as intuitive as possible (for example, if Fusion were to automatically apply Make Uniforms at regular intervals, this would likely introduce more unexpected shape changes, not less). But as an advanced user, it's somewhat helpful to be aware of this concept at least, if only to recognise when this might be responsible for unexpected shape issues, and therefore knowing when it's useful to apply a Make Uniform.
Hope this helps clarify the behaviour, and let me know if you had any questions about this.
Thanks,
Jake

Jake Fowler
Principal Experience Designer
Fusion 360
Autodesk