Is there such a thing as a truly clear oil based polyurethane? I know they yellow over time, but don't they also apply amber?
There are lighter and darker oil-based polys (and other varnishes, not all oil-based varnishes contain polyurethane) but essentially all are various shades of yellow. This is inherent to the product because they're oil-based, that base oil is almost invariably slightly yellow. But also refer to the Note below.
Broadly speaking the clear finishes — sometimes referred to as "water clear" or "water white" — are either waterbase varnishes (very different to oil-based) or a type of solvent finish (i.e. lacquer).
Note: quite a bit of the colouring that oil-based varnishes provide to wood is not due to them being yellowish. Put simply the effect is similar to what happens when you dampen wood with mineral spirits, which immediately gives a "deeper" or "richer" tone despite mineral spirits being completely clear.