Can I flush patch a speaker box on a wall with spackle for wallpaper
In order to recess the blank cover plates into your drywall, you could try finding the smallest blank cover you can get. They do make them in smaller and larger sizes, though you may need to shop around a bit.
Once you found one that's smaller than what's on there now, install it on the box, and mark the outline on the wall. Remove the plate, trim the drywall around your markings, and re-install the blank cover. It will now be recessed behind the drywall, unless the box itself is exactly flush or protrudes out.
Now you could use tape and drywall mud to make the area flush and apply whatever covering you would like.

Alternatively, you could also remove the boxes completely, for example, by using a saw to cut through the nails that hold them to the joist and then pulling them through the hole. You would then place a thin, short board through the opening (like a piece of 1x4 ripped to fit easily, or plywood), and use that to fix some cut-out drywall into the hole, and then patch as you normally would.
It would look something like this before you place the patch piece over the wood: