ADDED: To be clear, (1) I can see why such (perhaps sloppy) notation can be confusing and it's quite natural that many would find it confusing at first and I used to too and (2) nonetheless I believe that there is a value in this type of abuse of notation. But yes it demands explanation. I will first explain in generality (which you probably know, but for others who might ask the same questions) and then get to your specific questions.
$dx, dt, dy$. There are two crucial points to be made about this kind of notation.
First, this style of notation is referring to the intuition of variables and infinitesimals.
Let's say you come across something like the following argument:
Consider the unit circle. This is defined by $$x^2 + y^2 = 1$$ By
differentiating, we can see that the following relation holds on the
unit circle: $$2 x dx + 2 y dy = 0$$ Therefore, the circle has the
property that blah blah.
Note how the argument uses $dx, dy$ liberally as if they are well defined actual quantities. When a mathematician is reading the middle part of that argument, he might intuitively interpret it as follows (let's take aside its possible formal meanings for a moment):
If $(x,y)$ is an arbitrary point on the unit circle and if $(x+dx, y+dy)$ is another point on the circle extremely close to $(x,y)$, then
the four numbers $x, y, dx, dy$ have the property that $2 x dx + 2 y dy$ is extremely close to $0$ (compared to $dx,dy$).
Actually, he could be visualizing $(x,y)$ as continuously changing for the duration of one second, and maybe divide the duration of one second into million steps (the duration of each step is one millisecond). For example, he could imagine the value of $(x,y)$ as changing from $(0,1)$ (the north pole) to $(0, -1)$ (the south pole) while going down the right side of the circle. For each step, if $(x,y)$ is the position of the moving point at that moment and if $(x+dx, y+dy)$ is the position at the next moment (the next step), then the four numbers $x, y, dx, dy$ have the property that $2 x dx + 2 y dy$ is extremely close to $0$.
As for its possible formal meanings, depending on his preference or context, the mathematician could for example take its meaning to be a statement about differential forms, or a statement about parametrized curves (representing the circle), or maybe just a geometric statement about tangents to the circle.
For the substitution in your post, the starting relation is $u = \sin t$. You are supposed to imagine the value of the pair $(t, u)$ continuously changing from $(a, \sin a)$ to $(b, \sin b)$ along the sin curve, say for the duration of one second. It does not matter if $b$ is smaller than $a$ or not. It does not matter whether $u$ happens to take some specific value, say 0, more than once between the initial moment $t =a$and the last moment $t = b$. It does not matter if the movement is by constant speed or not. We could even change direction at some moment then change direction again at another moment. The only thing that matters is that you can imagine some movement that starts from $(a, \sin a)$ and finishes at $(b, \sin b)$ and along the curve. Now divide into million steps. For each step, if $(t,u)$ is the position of the moving point at that moment and if $(t+dt, u+du)$ is the position at the next moment, then the four quantities $t,u,dt,du$ have the property that $du$ is extremely close to $\cos t dt$.
Second, it is a good thing to use an argument that uses $dx, dt, dy$ liberally as if they are well defined things, as long as the user (of the argument) and the reader can easily come up with a way to convert the argument into a rigorous argument free of such liberal use. This could be done by using the notion of parametrized (differentiable) curves and/or Riemann–Stieltjes integral in most cases. For the case in your question, conversion is much simpler, as demonstrated in some other answer, or as you noted in your post. Of course, it's also worth noting that one can come to nonsensical conclusions by reasoning about infinitesimals in an unregulated way, as demonstrated with the famous "proof" of $1 = \sqrt{2}$. Hence the "as long as" clause.
To answer your question about the notation $\int_{t=a}^{t=b} u du$. Again, imagine the value of $(t,u)$ changing from $t=a$ to $t=b$ along the curve for the duration of one second. Divide the duration into million steps.
Pretend that the expression
$$\int_{t=a}^{t=b} u du$$
just means the result you get when you sum $u du$ during this one second. Think of this as a sum of million terms: one term for each moment. Yes this expression only makes sense when a specific substitution like $u = \sin t$ is agreed upon beforehand. The formal meaning of the expression should be obvious from the intuition.
The expression
$$[\frac12 u^2]_{t=a}^{t=b}$$
means the value of $\frac12 u^2$ at the last moment minus that at the first moment. This expression too only makes sense when a substitution is agreed upon.
We can also pretend that the expression
$$\int_a^b \sin t \cos t dt$$
means a sum of million terms: one term for each moment. For each moment, $\sin t \cos t dt$ is added. $\sin t \cos t dt$ is (almost) equal to $u du$ at each moment, and that is the intuition behind:
$$\int_a^b \sin t \cos t dt = \int_{t=a}^{t=b} u du$$
At each moment, $u\, du$ is (almost) equal to the value of $\frac12 u^2$ at that moment minus the value of $\frac12 u^2$ at the next moment. This is usually expressed as
$$d(\frac12 u^2) = u\, du$$ and you can take its formal meaning to be that $\frac12 u^2$ is an anti-derivative of $u\, du$ and so we can write (by the formal meaning, or by the intuition):
$$\int_{t=a}^{t=b} u du = [\frac12 u^2]_{t=a}^{t=b}$$