I've used techniques akin to those explained at the link:
http://www.apple.com/quicktime/tutorials/embed.html
that you mention. You should be concerned about it if you don't want IE Windows users having to 'click and/or hit spacebar to activate this control'.
QuickTime is not backward compatible unless saved as such. If you take advantage of the more efficient recent compression algorithms and/or the higher quality graphics rendering techniques, your movie can only be successfully experienced in a browser equipped with a recent enough version of QuickTime capable of decoding it.
Your code:
<object classid="clsid:02BF25D5-8C17-4B23-BC80-D3488ABDDC6B" width="Wpx" height="H+16px" codebase="http://www.apple.com/qtactivex/qtplugin.cab#version=6,0,2,0">
<param name="controller" value="TRUE">
<param name="type" value="video/quicktime">
<param name="autoplay" value="true">
<param name="target" value="myself">
<param name="src" value="URL">
<param name="pluginspage" value="http://www.apple.com/quicktime/download/indext.html">
<type="video/quicktime" BGCOLOR="#000000" BORDER="0" PLUGINSPAGE="http://www.apple.com/quicktime/download/indext.html"></EMBED></object>
I think you meant to have this:
<EMBED type="video/quicktime" BGCOLOR="#000000" BORDER="0" PLUGINSPAGE="http://www.apple.com/quicktime/download/indext.html"></EMBED>
Has no opening embed tag but does have a closing one. Movies can now be put on a page (for modern browsers only) using two object tags (with slightly differing syntax) instead of an object and an embed but having only a closing embed tag, as you do, will probably cause problems.
The placement of the code is similar to that of an image or paragraph or any other HTML element. Unless absolutely positioned, it will appear in the normal flow of the layout of the page.