The best thing you could do is instead of having dune2 starting full screen in its native resolution (and thus forcing your monitor to change to a very low resolution, and if it is a TFT monitor, apply some kind of scaling of its own, that for one reason or another stays after you leave the game) you could set the resolution of the game to match your screen resolution and then apply scaling to it, i.e. make a custom dosbox.conf file especially for the game, and set
where width and height are the dimensions of your monitor's resolution
and the scaler
to one of these
Check the wiki page and decide for youself which filter suits you (or the game) best.
normal2x, normal3x, advmame2x, advmame3x, advinterp2x, advinterp3x, hq2x, hq3x, 2xsai, super2xsai, supereagle, tv2x, tv3x, rgb2x, rgb3x, scan2x, scan3x
and then in the autoexec section of the file
you mount the game's folder and start the game.
Then you can make a custom desktop file that calls the game like this for example
You can find the conf file that dosbox uses by default in the ~/.dosbox folder and use it as the template for you own custom conf file.
dosbox -conf ~/Games/Dune2/dosbox_dune2.conf
If the above seem a little complicated to you, then you could use a graphical dosbox frontend like dbgl to setup the game.
Hope that helps.