What exactly is the problem? This seem to work fine.
\documentclass[a4paper]{report}
\usepackage{classicthesis}
\usepackage[left=4.3cm,right=4.3cm,top=5cm,bottom=4.7cm,includehead,includefoot]{geometry}
\usepackage{lipsum}
\begin{document}
\title{Lorem ipsum}
\author{Patrick Happel}
\maketitle
\chapter{Part 1}
\lipsum
\end{document}
There are not random results but inconsistent settings. Please use the option showframe in the package geometry and see the log file to understand what happen with your settings.
Take into account that top margin in Lyx should be 15 mm plus headheight plus headsep and that header text should be enough small to fit in the headheight, otherwise LaTeX will change his setting trying to do the best.
In the same way, bottom margin should be 15 mm plus the footskip, but the footer text must fit within the foot skip.
Taking this into account, you can already fix without problems the margins using the normal menu of LyX (Documents>Settings...>Page Margins), but there are nothing wrong checking "Defaults Margins" box and using the package geometry directly in Documents>Settings...>LaTeX preamble. This allow you to use options of geometry that LyX cannot manage, or use dynamic dimensions, so the margins are calculated correctly independently of the default font size:
\documentclass{article}
\usepackage[paperheight=16cm,paperwidth=14cm,showframe]{geometry}
\geometry{
lmargin=15mm,
rmargin=15mm,
tmargin=\dimexpr15mm+1.5\baselineskip,
bmargin=\dimexpr15mm+1.5\baselineskip,,
headheight=\baselineskip,
headsep=.5\baselineskip,
footskip=1.5\baselineskip}
\usepackage{lipsum}
\usepackage{fancyhdr}
\pagestyle{fancy}
\begin{document}
\section{Testing margins}
\lipsum*[1]\footnote{A foonote}
\lipsum*[2]\footnote{A foonote}
\lipsum*[3-5]
\end{document}
Some like \chead{\Huge A} just at the end of the preamble will ruin this layout, but LaTeX warn you in the .log file:
Package Fancyhdr Warning: \headheight is too small (12.0pt):
Make it at least 30.0pt.
We now make it that large for the rest of the document.
This may cause the page layout to be inconsistent, however.
Also, as you can see in this MWE, the footnotes are not a problem at all, since they are included in the text area, not in the margins.
On the other hand, for a 12pt article the default font size in footnotes (\footnotesize) is 10pt, so you must use a \scriptsize. See What point (pt) font size are \Large etc.? and Set font size for footnotes.
Best Answer
Here is one option, using
geometry. Add the following to your preamble:This sets all margins (top, bottom, left and right) to be 54pt on an A4 page (use
paper=letterpaperif you're using US Letter size). Additionally, the margins are set to include the header and footer as part of the specification. This, however, doesn't meet the requirements for the first page, which has to have a top margin of 72pt (18pt more than the other pages). For this, I'd insert an appropriate vertical adjustment on the first page by also addingsomewhere within your document preamble.