A flaw in the premise
$x=\tan t$ satisfies the differential equation $\dfrac{\mathrm{d}x}{\mathrm{d}t}=x^{2}+1$.
So it would seem that "$\dfrac{\mathrm{d}}{\mathrm{d}x}\left(\dfrac{\mathrm{d}x}{\mathrm{d}t}\right)$
for $x=\tan t$" is $\dfrac{\mathrm{d}}{\mathrm{d}x}\left(x^{2}+1\right)=\boxed{2x}$ and/or $\boxed{2\tan t}$.
But $x=\tan t$ also satisfies the differential equation $\dfrac{\mathrm{d}x}{\mathrm{d}t}=\sec^{2}t$.
So it would seem that "$\dfrac{\mathrm{d}}{\mathrm{d}x}\left(\dfrac{\mathrm{d}x}{\mathrm{d}t}\right)$
for $x=\tan t$" is $\dfrac{\mathrm{d}}{\mathrm{d}x}\left(\sec^{2}t\right)=\boxed{0}$.
Those calculations can't both be right. And there's not really
a reason to choose one over the other. So what would make the most
sense, and what is the case, is that they're both wrong. "$\dfrac{\mathrm{d}}{\mathrm{d}x}\left(\dfrac{\mathrm{d}x}{\mathrm{d}t}\right)$
for $x=\tan t$" is meaningless, so it's actually good that the
OP didn't have intuition for it.
How can we think about things?
As with many things in calculus, this is a situation where the notation
can cause confusion. I'll rephrase things without any Leibniz notation
and then come back to it later.
$\varphi'(t)=\varphi(t)-t$ is a differential equation, and the functions
$\varphi(t)$ that satisfy it on an interval are of the form $\varphi(t)=1+t+ce^{t}$
for a constant $c$. There is a function of two variables that can
help us talk about this differential equation: $f\left(x,t\right)=x-t$.
It lets us write the differential equation as $\varphi'(t)=f\left(\varphi(t),t\right)$.
By changing the function $f$, we can get different differential equations
$\varphi'(t)=f\left(\varphi(t),t\right)$. And it turns out there
are theorems like Picard-Lindelöf that tell us things about solving
the differential equation if we know things about the function $f$.
Since $f$ is a function of two variables, it doesn't have a derivative
we can call $f'$. Instead, it has two "partial" derivatives:
$f_{1}$ where we only care about changes in the first coordinate
(and treat the second as a constant) and $f_{2}$ for the second coordinate.
We have, for every pair of numbers $(a,b)$, $f_{1}\left(a,b\right)={\displaystyle \lim_{h\to0}}\dfrac{f\left(a+h,b\right)-f\left(a,b\right)}{h}$.
By letting $a$ and $b$ vary, we can think of $f_{1}$ as its own
function of two variables, that you might write $f_{1}\left(x,t\right)$.
Picard-Lindelöf says that if $f$ and $f_{1}$ are continuous (which
isn't as simple as "continuous" for a function of one variable)
in a region around a point $\left(x_{0},t_{0}\right)$ then we are
guaranteed a unique solution to $\varphi'(t)=f\left(\varphi(t),t\right)$
at least on a tiny interval around $t_{0}$.
Note that $f\left(\varphi(t),t\right)$ depends only on $t$. It only
has one input, so we cannot talk about different partial derivatives
of $g_{f,\varphi}(t)=f\left(\varphi(t),t\right)$. We could
look at $g'(t)$, but that would be $\varphi''(t)$.
Translating to Leibniz notation
If we write $X=\varphi(t)$, then $\varphi'(t)=\dfrac{\mathrm{d}}{\mathrm{d}t}\varphi(t)=\dfrac{\mathrm{d}}{\mathrm{d}t}X=\dfrac{\mathrm{d}X}{\mathrm{d}t}$.
I'm using a capital $X$ because I don't want to confuse this "dependent
variable" with the independent variable $x$ in $f\left(x,t\right)$.
If $X=\varphi(t)$ is a solution to the differential equation, we
have that $X$ satisfies $\dfrac{\mathrm{d}X}{\mathrm{d}t}=f(X,t)$.
The partial derivative $f_{1}(x,t)$ is often written $\dfrac{\partial}{\partial x}f(x,t)$.
The "curly $d$" is used to suggest that there is at least one
independent variable other than $x$. (Also note that nothing in a
discussion of the Picard-Lindelöf theorem talks about substituting
$X=\varphi(t)$ in for $x$ in the expression $\dfrac{\partial}{\partial x}f(x,t)$.)
What went wrong?
We need to be very clear on what a phrase like "$x=\varphi\left(t\right)$
satisfies $\dfrac{\mathrm{d}x}{\mathrm{d}t}=f\left(t,x\right)$"
means. Something like $\dfrac{\mathrm{d}}{\mathrm{d}t}\varphi\left(t\right)$
(e.g. $\dfrac{\mathrm{d}}{\mathrm{d}t}\tan t=\sec^{2}t$) will just
have $t$s in it and never have $x$s, so the phrase can't generally
mean "if you substitute in $\varphi(t)$ for $x$ on the left side,
you get the right side". It has to mean "if you substitute in
$\varphi(t)$ for $x$ on both sides, it's true". Since a solution
for $x$ like $\varphi(t)$ is a function of $t$, and $\dfrac{\mathrm{d}x}{\mathrm{d}t}$
has no $x$ in it, we shouldn't write $\dfrac{\mathrm{d}}{\mathrm{d}x}\left(\dfrac{\mathrm{d}x}{\mathrm{d}t}\right)$.
Nor should we use the partial derivative notation $\dfrac{\partial}{\partial x}\left(\dfrac{\mathrm{d}x}{\mathrm{d}t}\right)$.
While we may write the differential equation as "$\dfrac{\mathrm{d}x}{\mathrm{d}t}=f(x,t)$",
the only independent variable in $\dfrac{\mathrm{d}X}{\mathrm{d}t}=f(X,t)$
is $t$, since $X=\varphi(t)$ depends on $t$. So $\dfrac{\partial}{\partial x}\left(\dfrac{\mathrm{d}x}{\mathrm{d}t}\right)$
is either completely undefined, or always $0$ (if you interpret something
like $\sec^{2}t$ as depending on both an independent variable $x$
and $t$).
The point of confusion
The key point is that $x$ is used as an independent variable in "$\dfrac{\partial}{\partial x}f(x,t)$",
but used as a dependent variable (hiding an expression $\varphi(t)$) in "$\dfrac{\mathrm{d}x}{\mathrm{d}t}=f(x,t)$".
That difference is subtle and can lead to confusion. But Leibniz notation
is common and nicer for doing calculations, so we just have to watch out for
issues like this.