The diagram you've plotted is a color-magnitude diagram, and the magnitude it plots is the apparent magnitude.
If you click the Plot2D button and select the plot type, under "Astrophysical parameters" you will find "GDR2 HR diagram". This produces a plot that looks like this:
This is probably somewhat closer to what you are expecting. It isn't the same shape as the HR diagrams in the question because its missing hot stars and cooler objects. As noted in the Gaia DR2 contents page:
Subject to limitations (see below) the effective temperatures Teff for more than 161 million sources brighter than 17th magnitude with effective temperatures in the range 3000 to 10,000 K.
The limitations section goes on to state:
The values of Teff, extinction AG, reddening E(GBP-GRP), radius, and luminosity were determined only from the three broad-band photometric measurements and the parallax on a star-by-star basis (parallax was not used for Teff though). The strong degeneracy between Teff and extinction/reddening when using the broad band photometry necessitates strong assumptions in order to estimate their values. One should thus be very careful in using these astrophysical parameters and refer to the papers and online documentation for guidance.
I haven't seen a way to set custom axes, it looks like you can only create the predefined plots, so it doesn't look like you can do absolute G magnitude against GBP-GRP.