Different math font need different treatment, I'm afraid. But we can use a couple of parameters in order to adjust the positioning for a particular font.
\documentclass{article}
%\usepackage{unicode-math}
%\setmathfont{STIX Two Math}
%\setmathfont{TeX Gyre Pagella Math}
\makeatletter
\DeclareRobustCommand{\noteta}{\mathrel{\mathpalette\noteta@{\noteta@kern\noteta@raise}}}
\newcommand{\noteta@}[2]{\noteta@@#1#2}
\newcommand{\noteta@@}[3]{%
\mkern#2
\ooalign{\hidewidth\raisebox{#3\height}{$#1\m@th/$}\hidewidth\cr$#1\m@th\mkern-#2\eta$\cr}%
}
\newcommand{\noteta@kern}{1mu}% tailor to the font
\newcommand{\noteta@raise}{-0.1}% tailor to the font
\makeatother
\begin{document}
$a\notin A$
$a\noteta A$ $\scriptstyle a\noteta A$
$a\mathrel\eta A$ $\scriptstyle a\mathrel\eta A$
\end{document}
Output with pdflatex

Output with Latin Modern Math
Just loading unicode-math (uncomment line 2)

Output with STIX Two Math
Uncomment lines 2 and 3

Output with Pagella Math
Uncomment lines 2 and 4

This probably needs a different amount of raising/lowering. Changing \newcommand{\noteta@raise}{-0.1} into
\newcommand{\noteta@raise}{0}
results in

Advice
Experiment with the math font you use, but do remember that \mathrel\eta is needed if you want to use the symbol as a math relation.
\not\eta? ?% harmless under LuaLaTeX, required for pdfLaTeXis referring to, but if you mean the line above, thenT1encoding should (almost)never be used with luatex it breaks all the unicode support, so not exactly harmless, andutf8is not required for pdflatex, unless your latex is 10 years old