I'd be afraid of concrete-type construction leveler.
When the boat flexes, and they always do,
this stuff will crack and break if the boat is stronger
or will make a "hard spot" on your hull
if the filler
is deep enough to make it the stronger.
Either way I see only disappointment.
If the low spots are more than a few litres in volume
I like the idea of glassing in a cover piece.
I wouldn't use plywood
, though, unless I was confident
that it was going to stay permanently dry.
It isn't difficult to make a GRP panel for the cover.
Just cover an appropriately sized flat surface
laid across two sawhorses)
with waxed paper or some other easy-release substrate
and wet out several layers of glass cloth or roving
until you reach the desired thickness.
Next morning you cut it to fit and glass it in place
with glass strips and resin around the hull/cover joint.
My own bilge required some serious levelling
and that's how I handled the deep bits.
For shallower areas I mixed resin with styrofoam beads
and poured/troweled that to the level I wanted.
This is simplified a bit, of course.
If working with GRP is a new technology for you
I'd be glad to exchange detailed info via email
I'm no expert but I have learned a few things the hard way.
The hardest part of building your first boat...
is building so much of it TWICE!