Hi Kedu,
The coaxiality issue with countersinks is a valid concern, especially if the process used to create the countersink allows this type of error.
If coaxiality of the countersink is a concern, then I think the only effective alternative is to "kill" (as you say

) the countersinks with profile of a surface.
If the mating surface of the part is planar and normal to the holes then it could be the primary datum feature for the profile tolerances. The secondary could be each respective hole, with "INDIVIDUALLY" specified by the datum feature symbol and the feature control frame. If the surface the countersinks are cut into is planar, that may make a better primary datum feature, because then the depth of the countersinks would then more reliably be ensured to keep the heads of the fasteners flush or below the surface, as is usually needed.
We could then consider each countersink to be well controlled relative to the hole it serves, or maybe overly controlled, or maybe "dead" due to the effects of feature control frame application
For most cases, the countersink tool pilots well enough on the hole though, so this may not be such a concern, at least for a floating fasteners type of application.
For a pattern of fixed fasteners though, the cylindrical holes hole becomes a clearance feature and the location of the countersinks is critical. This is especially true when relatively short, large diameter fasteners are used. For those cases the profile of a surface applied to the countersinks would not use each individual hole for the secondary datum feature. No secondary datum feature could then be best, with best fitting of the data to the pattern of countersinks as specified by basic dimensions, handing the location of each feature within the pattern. With the threaded holes in the mating part controlled by position at RFS with a similar datum reference frame, the screws should all tighten nicely without a bunch of tilting of screws and misalignment within the pattern of countersinks.
Dean