TeX uses fixed point arithmetic and TikZ exploits this.
Let's try in a different way. TeX computes the height of the box as 116.43562pt which is 7630725 scaled point (I asked TeX to show this). Similarly, 17.68pt is 1158676 scaled point. The subtraction is 6472049 scaled points.
Saying \dimen0=6472049sp and then \showthe\dimen0 results in TeX showing 98.75563pt because of how TeX arithmetic works. If we do with a calculator
116.43562*65536=7630724.79232
17.68*65536=1158676.48
so you see that TeX rounds up the first dimension and down the second one, which explains the difference in the fifth decimal digit.
Actually, TeX computes the height exactly as 7630725, but the shown value is the nearest value to the division by 65536 with five decimal digits. You can try:
\dimen0=116.43563pt \showthe\dimen0
to get
*\dimen0=116.43563pt \showthe\dimen0
> 116.43562pt.
Not all numbers with five decimal digits correspond to an integral number of scaled points.
The computation, as far as TeX is concerned, is exact. If you want to do floating point arithmetic, you can use \fpeval.
\documentclass{article}
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{pgf,tikz}
\newsavebox{\mybox}
\newlength{\myboxht}
\newcommand{\myfunction}[1]{%
\sbox{\mybox}{%
\begin{minipage}[b]{\linewidth}
#1
\end{minipage}%
}
\setlength{\myboxht}{\ht\mybox}%
\edef\pgfmathresult{\fpeval{round(\myboxht-17.68pt,5)pt}}%
\usebox{\mybox}
The height: \the\myboxht
Result of mathematical operation: \pgfmathresult
}
\begin{document}
\myfunction{
Test
\begin{tikzpicture}
\draw (0,0)--(5,3.3);
\end{tikzpicture}
Test}
\end{document}

But rounding always get in the way.