Bottom Layer Compression (over extrusion) - Can't get rid of it
The first thing that comes to mind is that, even though you have levelled the bed, the print nozzle may be too close causing too much "squish" on the first layer. Squish isn't bad as it promotes adhesion, but in your case, as you are looking for finer tolerances on the holes, it may be a problem. I use a feeler gauge and aim for 0.15&nbsp;mm gap when printing at 0.2&nbsp;mm layer height.

Next thing to consider is ensuring you have calibrated your flow rate/extrusion multiplier. See here for detailed procedure

Assuming flow rate is calibrated I can think of some settings in Cura that could affect your print.


Initial Layer Flow
Flow Rate Compensation Factor
Combing Mode / Avoid Printed Parts


Initial Layer Flow enable the use of a higher/lower flow rate in you first layer. Typically I set this to a value larger that my flow rate, 120&nbsp;%, as I want good adhesion and am less worried about the elephant's foot effect. However, you could reduce it to less than your flow rate although that may compromise adhesion unless you use a brim.

Flow Rate Compensation Factor For most circumstances this should be 100&nbsp;% which indicates that your flow rate should be used as set and not compensated for. I would check that this value has not been altered cause over-extrusion.

Lastly, there are two travel settings. Combing Mode and Avoid Printed Parts work in combination to reducing the impact of travels in the finished print. I would ensure you have combing turned on (e.g. Not in Skin) and that you have enabled Avoid Printed Parts. More details on these settings can be found here