...does the mounting of the rudder mount have any negative effects with the handling of the kayak or steering ability when peddling only?
Under pedal power only, you can expect the drag from the motor to slow you down about .3 MPH +/- at "fast" cruise compared with the the conventional rudder. There is no problem with rudder control, although at that speed the prop whirs and there was a constant left rudder input. For silent operation, the prop stops spinning at about 2.5 MPH and starts up somewhere around 4 +/- MPH. This may vary from one unit to another and over time.
Is the twist & stow rudder with the "T" handles subjected to extra strain when lifting the rudder for shallow water?
You shouldn't have any difficulties. You don't need to lock the rudder down unless going backwards, so it will kick up over an obstruction (or you can haul it up ahead of time)
Installation note: Be sure to allow plenty of slack at the plug-in point to avoid creating any the pressure on the rudder line (below left) or strain on the plug (below, right):
So plan your hole locations accordingly.