I see one way to install PEX is with a manifold system - where 1/2" PEX
pipes run off of a manifold to each appliance.

Thats how our current house is done but the manifolds (one for HOT, one for
COLD) have no shut off valves on them.
Inline shut off valves in each cabinet

Instead of the manifold system - could we do it in the 'straight line'
fashion - using 3/4" PEX? Or is there something we are missing?

Yes, that works too. Thats how our last (1998) house was done..1" to3/4"
Pex, dropping down to half inch for each final line.
Angle stop shut off valves-No manifolds.

R