Does it matter if the remotely tuned capacitor is at the top or the
bottom
of the loop?

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In principle, it doesn't matter.

But it is important the capacitor is located diametrically opposite to
whatever arrangements there are to feed the loop.

Ideally the loop should, as far as possible, be isolated and be
allowed to find its own electric balance with respect to ground.

The capacitor itself is likely to be unbalanced with respect to
ground. So it it is better to place it as far as possible from the
ground and everthing else, i.e., at the top. The highest voltages are
concentrated at the ends of the loop connected to the capacitor.

It is best NOT to connect the main loop to the feedline. Use a small
coupling loop in the same plane as the main loop and about 1/5 of the
diameter if the coax is 50-ohms. For 75-ohm coax it is about 1/4 of
the diameter.

Isolating the main loop from the coupling loop and feedline prevents
RF current from finding its way on to the feedline.

If the capacitor motor is not very well isolated from the capacitor
itself then place an RF choke in the bunch of control wires near to
the motor. Bring the control wires down from the motor across the
loop diameter and in a neutral electric field. Anything which comes
down vertically across the diameter is in a neutral field. It could be
a metal mast to support the motor and, via the motor, the top of the
loop itself.

In general, having the capacitor at the bottom of the main loop is
more likely to unbalnce the capacitance of the loop to ground.
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Reg, G4FGQ.