From looking at your picture, the countersinks are definitely not deep enough.
You should not be able to see daylight between the adjoining pieces.
When joining any two or even three pieces of material, the overwhelming rule is to keep the fit tight without any gaps.
To gauge the depth of my countersinks, I made a test tool. Take a piece of scrap aluminum and dimple it to the correct size.
That is good advice!
Make your test tool for just one hole. By using a strip with several holes you might possibly introduce a poor line up of rivet holes to make it appear as though the countersink is not deep enough.
For me, a "very slightly" proud dimple would result in a perfect fit after a rivet was set. If you see light between the pieces after riveting, its not acceptable.
Although good general guidelines are provided in the building manual, precise
countersinking requires a bit of adjustment depending on the material and location of the material.
You may achieve a perfect countersink on a .063 piece of aluminum rested
on a bench and find that using the same setting on a flange produces a different result. The spar flange is unsupported and somewhat yields to the pressure you apply when machining the countersink. You'll need to support the flange with your fingers or a piece of backing and be consistent on how much down pressure you apply.
The good news is that your countersinks appear to be too shallow and taking off more is much easier than dealing with the reverse problem.