Using the custom php code and your own template file should mean, that only this will be ptinted and nothing more, but YARPP still adds a few more things which breaks the design.
Something I don't understand, before the template file appears a number, either 1, 2 or 3, which I don't even know where it comes from, but the design breaks, because YARPP is closing one div container too much, so as a workaround a had to add an opening div inside the YARPP template file, which solved it, but if there are no related posts, this is not necessary. Weird things.
I had a look at the code, "class-core.php" shows the problem. Line 818 should only use the contens of the template-file and not append to the previous. Instead of
$output .= ob_get_contents();
it should be
$output = ob_get_contents();
Next problem is the closing div which is always appended in line 844, which is not necessary if I use my own template. Should be put in an if-statement, which doesn't print it with a template.