When we substitute $x=\sin(t)$ into $$\int \sqrt{1-x^2}dx,$$ why we only take the "$+$" sign even though $\sqrt{1-\sin^2(t)}=\pm \cos(t)\;?$
EDIT: Thank you to @Cameron Williams for the suggested problem. I know for the definite integral, we need to discuss carefully according to the quadrant for + or -, and that's no ambiguity. But here I want to ask for the indefinite case, where there is no specified quadrant, then why we only take the "+" sign?
EDIT: Thank you to @EeveeTrainer for the suggested problem. But here it is not exactly to take square root on a number, but a function. $\sqrt{4}=2$ is not the same as $\sqrt{\cos^2(x)}=\cos(x)$. Because $\cos(x)$ might be negative, depends on the quadrant of $x$ previously specified. Is the underneath assumption to choose a quadrant such that both $\sin$ and $\cos$ are positive, even though there is no quadrant specified for an indefinite integral?
EDIT: Thank you to @finch's comment on the conventional interval chosen for $\sin(x)$ (or $\cos(x)$) so that they are invertible. For $\sin(x), ~~[-\frac{\pi}2, \frac{\pi}2];$ for $\cos(x), ~~[0, \pi].$ So, if I want to use substitute $$x=\sin(\theta)$$ into $$I_2=\int \sqrt{x^2}\sqrt{1-x^2} dx,$$ which interval should I choose? Do I choose $$[-\frac{\pi}2, \frac{\pi}2]\cap [0, \pi] ~?$$
ADDENDUM
Say, I choose the domain for $\theta $ as $$[-\frac{\pi}2, \frac{\pi}2].$$ Then the integral becomes $$I_2=\int \sqrt{\sin^2(\theta)}\sqrt{\cos^2(\theta)} \cos(\theta)~d\theta=\int |\sin(\theta)|\cos(\theta) \cos(\theta)d\theta$$
$$\begin{align} \text{If}~~~ \theta\in[-\frac{\pi}{2},0],~~I_2&=\frac{1}{3}\cos^3(\theta)+C=\frac{1}{3}(1-x^2)^{3/2}+C\\ \\ \text{If} ~~~\theta\in(0,\frac{\pi}{2}],~~I_2&=-\frac{1}{3}\cos^3(\theta)+C=-\frac{1}{3}(1-x^2)^{3/2}+C \end{align}$$
Why do we usually choose only the bottom solution?
In the substitutions $x=\sin t$ and $x=\sin\theta,$ you don't have to restrict your values of $t$ or $\theta$ to any particular interval. You do need to make sure that whatever values of $t$ or $\theta$ you allow, the formulas you use are equivalent to the original integral.
For the substitution $x=\sin t$ in $$ I_1 = \int \sqrt{1-x^2} \,\mathrm dx, $$ it is convenient to let $-\frac\pi2 \leq t \leq \frac\pi2$ because this is a very familiar part of the domain of the sine function and it covers all the values of $x$ at which the integral could possibly be evaluated (since we must have $1 - x^2 \geq 0$). But it is not necessary to do that. In order to use any real number as $t,$ you just have to recognize that in general, $$ \sqrt{1 - \sin^2 t} = \lvert \cos t \rvert, $$ and remember that you cannot just write $\cos t$ on the right-hand side because $\cos t$ is negative for many real values of $t.$ You end up with
$$ I_1 = \int \lvert \cos t \rvert \cos t\,\mathrm dt = \begin{cases} \int \cos^2 t\,\mathrm dt & \cos t = \sqrt{1 - x^2} \geq 0, \\ -\int \cos^2 t\,\mathrm dt & \cos t = -\sqrt{1 - x^2} \leq 0. \\ \end{cases} $$
You can choose either case for $\cos t$ ($\geq0$ or $\leq0$), just as long as you remember which case you chose and make the correct reverse substitution at the end. You'll get the same result either way, as you can confirm yourself. There's no need to be concerned with which quadrant $t$ is in, only with how to deal with the absolute value sign that taking a square root of a square requires.
It is similar for $$ I_2=\int \sqrt{x^2}\sqrt{1-x^2} \,\mathrm dx. $$ It is a fact that $$ \sqrt{\sin^2 \theta} \sqrt{\cos^2 \theta} = \lvert \sin \theta \rvert \lvert \cos\theta \rvert = \lvert \sin \theta \cos\theta \rvert,$$ so $$ I_2 = \int \lvert \sin \theta \cos\theta \rvert \cos\theta\,\mathrm d\theta = \begin{cases} \int \sin\theta \cos^2\theta\,\mathrm dt & \sin\theta\cos\theta = x\cos\theta \geq 0, \\ -\int \sin\theta\cos^2\theta\,\mathrm dt & \sin\theta\cos\theta = x\cos\theta \leq 0. \\ \end{cases} $$ That is, you use the first case when $x$ and $\cos\theta$ have the same sign, but use the second case when $x$ and $\cos\theta$ have opposite signs. That is, for the first case you can replace $\cos\theta$ by $(\operatorname{sgn}x)\sqrt{1 - x^2}$ (same sign as $x$) and in the second case you can replace $\cos\theta$ by $-(\operatorname{sgn}x)\sqrt{1 - x^2}$ (sign opposite to $x$). The final result will be the same either way, as you can verify.
Again, up to this point we have no need to be concerned about quadrants or intervals, only about the correct use of absolute value when taking the square root of a square. There is an extra complication in this case, however, because the naïve substitutions for $\cos\theta$ above do not match at $x = 0.$ If you want a single antiderivative that is continuous for $-1 \leq x \leq 1$ you have to play some additional games with the integration constant.