I don't have Pluma or VScode, but on my system GTK2 Geany and GTK3 Geany and Xed (the simple editor provided by the distro, which is GTK3 based) all are exactly the same size on the same standard (not hidpi) monitor all with a deja-vu mono font at the same point size. In other words Geany has the same size as other GTK renderers here. Not sure why Pluma (a GTK2 program) would be different unless it manipulates the chosen font size in some way.

I can believe that the VScode renderings will look different because, being web technology based, its not going to be using the GTK renderers. It also may do anti-aliasing differently which can make it look "bolder". Rendering a font is surprisingly not an exact science IIUC.

As is pointed out above there is a PR #407 to add fractional sizes, but it requires the maintainer to approve that the changes they requested have been done, and for it to be tested. You could test it if you can to help it along.

Also, Not only the sizes doesn't match, but also the spacing between the lines are very tight, which could be eye straining for some people

Line spacing is set by colour schemes in their line_height setting with the default value being in filetypes.common if the scheme is silent, which you can edit by Menu->Tools->Configuration Files->filetypes.common

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