Consider the following MWE:
\documentclass{standalone}
\usepackage{tikz}
\usetikzlibrary{calc}
\usetikzlibrary{positioning}
\usetikzlibrary{fit}
\usetikzlibrary{3d}
\makeatletter
\tikzset{
fitting node/.style={
inner sep=0pt,
fill=none,
draw=none,
reset transform,
fit={(\pgf@pathminx,\pgf@pathminy) (\pgf@pathmaxx,\pgf@pathmaxy)}
},
reset transform/.code={\pgftransformreset},
}
\makeatother
\tikzstyle{dr} = [draw, rectangle, line width=1pt, font=\Huge, align=left]
\tikzstyle{cl} = [>=latex,->,line width=1pt]
\begin{document}
\begin{tikzpicture}[
% x={(0.5cm,0.5cm)}, y={(1cm,0cm)}, z={(0cm,1cm)},
% every node/.append style={transform shape},
]
\draw[very thick] (0,0) rectangle (18,8) node[fitting node] (starter) {};
\begin{scope}[
shift={(1,1)},
% canvas is yx plane at z=0.25,
]
\node[dr] (NodeA) at (1,5) {Node A};
\draw[dr] (4.5,2.5) rectangle (11,6.5) node [fitting node] (NodeB) {Node B\\Slightly bigger};
\node[dr] (NodeC) [above=10pt of NodeB.south, anchor=south] {Node C};
\draw[cl] (NodeA) -- (NodeB);
\draw[cl] (NodeA) |- ($(NodeB.north west)-(10pt,10pt)$) -- ($(NodeB.south west)-(10pt,7.5pt)$) -| ($(NodeC.south west)+(10pt,0)$);
\end{scope}
\end{tikzpicture}
\end{document}
If I compile it as it is, I get the expected arrangement of nodes and connecting lines:

But if I enable 3D by uncommenting the commented lines in the MWE, I get this:

The NodeB text not being in perspective doesn't bother me all that much; what bothers me is that coordinates based on the NodeB fitting node rectangle do not work properly under 3D transformations (note that all is OK between "proper" nodes, e.g. the piece of the line going right into NodeC).
(I'm aware that this example, in particular, can be otherwise done without the fitting node rectangle - and so problem solved; the thing is, those are quite useful for GUI editing in TikzEdt, and so I have code with a ton of these all over the place; which is why I'd rather have a solution like a fix to the "fitting node" style instead. )

