I use mechanical wedge type bolts in our salt mine with stainless acorn nuts on the end. They will work in concrete too.
What about using something like this? I set them for control and boundary work with a brass washer in concrete. Not sure if it'll help you or not, but here is a link and it is rounded on top (or bottom in your situation).
You could try something like this.
http://www.ustoolandfastener.com/grk-caliburn-ph-handy-pak-1-4-x-2-1-4-50-pcs-57831/?gclid=Cj0KCQjw9uHOBRDtARIsALtCa94w53idpDNknfUN9KsW2oZVsaeazbBUZX1Aq62UJ-zn2nkYhLV29HAaAos_EALw_wcB
I wouldn't bother with epoxies at all, assuming the only purpose of the bolts are for survey control. Epoxies tend to be slow and messy, and when set in ceilings might slip a hundredth or so.
Redhead hammer set bolts would do the job without epoxy, they run about $0.50 each, and meet your rounded and unobtrusive requirements. Old rawl buttonheads would actually be perfect, but haven't been sold in the US for a decade or so. The third option would be to purchase a slightly undersized drill bit for the bolts, and just thread them directly into the rock.
As far as drilling and cleaning go, out of round or flared holes only really occur in hand drilling. Power drills makes a damn fine hole. A bottle brush should be the only other tool you need for ceiling holes (blow out bulb also needed for walls and floors), but honestly, as your holes are not structural, super clean really doesn't matter that much.
In my extremely limited tunnel experience, we would just set spads in natural ceiling cracks, saving us from the noise and weight of a drill.
EDIT: the first link provided by Taco Bell Dawg is similar to the old Rawl Buttonheads.
Question because I have no experience with a digital level. Is reading an upside down rod a standard feature for them?
You have to tell the level the shots are inverted. It will not read it inverted unless that function is enabled. Once it is enabled, it will not read it right side up until that function is turned off.