CommonMark seems to work for me instead of the built in Markdown. It works in many situations where Markdown doesn’t work: CommonMark Math in Pluto
I had to remove the comments in the latex since they seemed to break the parser but worked fine after that.
# ╔═╡ d1657bc0-61e4-4129-9dd5-7bd7e89a3629
using CommonMark
# ╔═╡ f23b0978-7f30-47b1-b6bd-dbb72c25b82f
cm"""
``
\begin{align}
f(x) &= ax^2 + bx + c \\
&= \begin{array}{c c}
& \begin{array} {@{} c c c @{}}
u_1 & \cdots & u_q
\end{array} \\
\begin{array}{c}
e_1 \\ \vdots \\ e_n
\end{array}\hspace{-1em} &
\left(
\begin{array}{@{} c c c @{}}
u_{11} & \cdots & u_{1q} \\
\vdots & & \vdots \\
u_{n1} & \cdots & u_{nq}
\end{array}
\right) \\
\mbox{}
\end{array}
&= ax^2 + bx + c
\end{align}
``
"""