You are mixing stuff.

First of all - there is energy conservation. Sure you can spontaneously create pairs of particle-antiparticle, but it requires energy - which can come from thermal fluctuation (Boltzmann distribution etc.), see sine-Gordon "Rubber Band Model of the Universe" - energy of random fluctuations create lots of kink-antikink pairs:

https://www.youtube.com/watch?v=nl5Qq5kUbEE [nofollow]Regarding mass of the field - all fields have inertial mass: you need to invest some energy to e.g. make it move (give kinetic energy).

From the other side, "dark energy" can have purely thermodynamical nature - be a random noise/fluctuations. Like 2.7K random noise of EM degrees of freedom, but of other degrees of freedom: corresponding to weak, strong and gravitational degrees of freedom - this kind of noise is tough to directly observe.

Regarding baryons, we need to understand their structure and sure only a small fraction of energy of this structure corresponds to the charges (quarks).

What structure is it? We need a stable structures like a vortex - they are generally called solitons.

Here is the one I consider:

http://fqxi.org/community/forum/topic/1416 [nofollow] , slides:

http://dl.dropboxusercontent.com/u/12405967/soliton.pdf [nofollow] Below is a s general picture of its speculation of baryons/nuclei structure:

So the basic structures of this model are lines having spin 1/2 configuration in cross-section (kind of Abrikosov vortex but in vacuum) and there are three types of them with growing energy density: electron, muon and taon spin loops.

This kind of magnetic 1D structures are observed in Sun's corona (

https://en.wikipedia.org/wiki/Magnetic_reconnection [nofollow] ), and would allow to explain holding nucleus together against Coulomb repulsion (like He4 in the picture).

Electron is such electron spin line with 180 deg rotation inside - getting hedgehog configuration - topological charge which is interpreted as electric charge (Gauss-Bonnet theorem acts as Gauss law).

Baryons would correspond to such loop around spin line (like above) - geometry says that they have to be of different types (the lowest energy is for electron-muon) and that such loop enforces some partial internal rotation - a fractional charge ("quark").

So baryon structure itself requires some (fractional) charge - proton has only this charge (can be narrow), while neutron has to compensate it with opposite charges like in the picture - has to be wide - has larger energy ...

**getting intuitive explanation of why proton is lighter than neutron** (we still don't understand from QCD).

Next,

**deuteron is lighter than p + n** because they can share their single charge like in the figure.

The energy of charge structure (like 511keV) is tiny comparing to other energies in these structures - mainly of the stress between spin loop and line - which can be interpreted as gluons in pertubative approximation.