why can't the missing mass (evidence for dark matter) be matrioshka brains/dyson spheres? i know that the claim is that nucleosynthesis models say that the observed abundance of deuterium is too high for dark matter to be baryonic, but couldn't deuterium be a waste product of civilizations?  you say that postulating civilizations is not the simplest explanation, but isn't it far more complex to postulate that we are unique (or an invisible form of matter with exotic physics for which we have no evidence)?  even from a single seed civilization, galactic colonization times are in the hundred million year range, so we should expect some evidence of environmental manipulation everywhere we look.  given the need for civilizations to hide from predators, isn't eliminating EM interactions/emissions the best strategy?
 A: I might be talking non sense, but I'll try arguing with your logic. (Is there any physics to be answered in there?)
You're doing a lot more than just postulating civilization.


*

*You're postulating they are on every single galaxy where dark matter effects have been found. (I'm no astrophysicist, but I believe dark matter effects have been verified on every single galaxy where we've looked.)

*You're postulating they reached a stage of galactic colonization, (again) on every single one of these cases. Note that if this stage really is on the range of 100 million years (which seems to be pure speculation on your part) than it is so small compared to the age of galaxies. Considering the number of galaxies we've looked at, we should have found some that are not colonized "yet" (Statistically speaking).

*Not to mention, where did they get all the matter for that? Isn't dark matter density 3 times higher than ordinary matter density?

A: Physically, if you look at the low level of CMB anisotropy and the BAO power spectrum, you need some sort of mass that interacts gravitationally but is decoupled from the photons before recombination (i.e. - dark matter). Otherwise there would be no way to seed the galaxy formation that we see occuring at lower redshifts. That is to say, dark matter needs to be primordial, so that it can dodge Silk Damping and provide the graviational "cores" around which galaxies form.
Which would also imply that dark matter cannot be the construct of an alien civilization. 
A: *

*Typical Drake equations yield 100s of societies per galaxy.  Most probably end tragically but it would only take 1 to colonize a galaxy.  There has been enough time to colonize all(indeginous or cross galaxy).  

*Life grows exponentially and we have only characterized the dark matter in a fraction of the universe.  Perhaps all have been colonized, or the tiny galaxies too small to generate successfully life or too far to colonize yet have not been observed.  This is a testable hypothesis:  we will find tiny, isolated galaxies without dark matter.  

*Imagine a pre colonized galaxy with denser and sparser regions.  The least time and energy to colonize would be going from densest to densest region.  Another testable hypothesis:  dark matter is lumpy, continuous, and a different fraction per galaxy.  Some may be far more than 3x and others less.
As it stands now no model of physics explains the data.  Evolution works in the opposite direction of entropy (netting to a loss but there is no shortage of mass,  energy and time to play with before the heat death).   

A: "So even if every star in the universe had a dyson sphere around it, that would add up to, about, 110% of the regular matter we measure, but it needs to be >600%"
Great point. If dyson spheres were around several stars though, would they obscure the light and thus lower the amount of stars we are actually estimating? It's not so much the DS material itself that consists of the gravity of dark matter, it is of those stars hidden within the dyson spheres we are not accounting for.
