GeoBubbleChart Colors

Carl's answer is most likely what you are looking for as it limits what is in the background. But, if you are interested in changing how the background countries look, I would suggest using one of the variants of GeoStyling["CountryBorders"]. For example,

d = {Entity["Country", "Belgium"] -> Quantity[11429336, "People"], 
   Entity["Country", "Netherlands"] -> Quantity[17035938, "People"], 
   Entity["Country", "Luxembourg"] -> Quantity[583455, "People"]};

GeoBubbleChart[d,
 GeoBackground -> GeoStyling[
   {"CountryBorders", "Land" -> Gray, "Ocean" -> White, "Border" -> Black}],
 GeoRange -> GeoGroup[d[[All, 1]]]
]

The additional options also apply to "Coastlines", too.

The easiest way is to use Show to combine the two:

d = {Entity["Country", "Belgium"] -> Quantity[11429336, "People"], 
   Entity["Country", "Netherlands"] -> Quantity[17035938, "People"], 
   Entity["Country", "Luxembourg"] -> Quantity[583455, "People"]};

Show[
 GeoGraphics[{EdgeForm[Black], FaceForm[Black], 
   Polygon[GeoVariant[Entity["Country", "Belgium"], "PrincipalArea"]],
    Polygon[
    GeoVariant[Entity["Country", "Netherlands"], "PrincipalArea"]], 
   Polygon[GeoVariant[Entity["Country", "Luxembourg"], 
     "PrincipalArea"]]}, GeoScaleBar -> "Metric"],
 GeoBubbleChart[d, GeoBackground -> None, 
  GeoRange -> {{49, 53.6}, {2, 7.5}}]
 ]

countries = Entity["Country", #] & /@ {"Netherlands", "Belgium", "Luxembourg"};
populations = EntityValue[countries, "Population"];

We can also use GeoRegionValuePlot to style individual country polygons

grvp = GeoRegionValuePlot[Thread[countries -> Range[Length@countries]], 
   GeoRange -> {{49, 53.6}, {2, 7.5}}, 
   ColorFunction -> (Opacity[.5, ColorData[97][#]] &), 
   ColorFunctionScaling -> False, PlotLegends -> None];

and Show grvp with GeoBubbleChart using the option GeoBackground -> None:

Show[grvp, 
 GeoBubbleChart[Thread[countries -> populations], 
  ChartBaseStyle -> Opacity[1], ColorFunction -> "Rainbow", 
  GeoRange -> {{49, 53.6}, {2, 7.5}}, GeoBackground -> None], 
 ImageSize -> Medium]

Alternatively, we can use Image @ grvp with the option GeoBackground:

GeoBubbleChart[Thread[countries -> populations], 
 ChartBaseStyle -> Opacity[1], ColorFunction -> "Rainbow", 
 GeoRange -> {{49, 53.6}, {2, 7.5}}, 
 GeoBackground -> {"Image", Image @ grvp}]