Font mismatch with Linux Libertine and siunitx package

This has nothing to do with siunitx: it's the font used for numbers in math mode that's wrong.

You can solve the issue with this block of font settings:

\usepackage[libertine]{newtxmath}
\usepackage[no-math]{fontspec}
\setmainfont{Linux Libertine O}

%%% Uncomment the following line, if something is still wrong    
% \DeclareSymbolFont{operators}{OT1}{LinuxLibertineO-LF}{m}{n}

The commented line might be needed, depending on the installed version of newtxmath.sty, which has undergone several changes in the last months.

The messages about checksum mismatches with LuaLaTeX are innocuous, albeit annoying.

with current TeXLive there is no problem. However, all font stuff depending to the old LaTeX loading mechanism should be done before you load the OpenType fonts:

[...]
\usepackage[libertine]{newtxmath}
\usepackage[no-math]{fontspec}
\usepackage{libertine}
[...]