Yes, the margins behave very similar in "normal" plotting mode and in multiplot mode. Basically, the margins can have three different "modes":
- Automatic, which is the default.
- Setting each margin to a specific size, like
set lmargin 2. The unit is character widths (or character heights for tmargin and bmargin).
- Setting a specific position of a border relative to the whole canvas, like
set lmargin at screen 0.1, which sets the left plot border at 10% of the total canvas width.
The only difference of the multiplot mode is, that the reference for the margins in 1. and 2. is given by the sites determined by the layout option:
set multiplot layout 2,2
This subdivides the whole canvas in four rectangles of equal size. Now, using
set lmargin 1
set rmargin 1
set tmargin 1
set bmargin 1
leaves a margin of one character width or height on each side of each subplot with respect to the smaller rectangles:
set multiplot layout 2,2
set lmargin 0
set rmargin 0
set tmargin 0
set bmargin 0
set format ''
plot x
plot x**2
plot x**3
plot x**4
unset multiplot

set multiplot layout 2,2
set lmargin 1
set rmargin 1
set tmargin 1
set bmargin 1
set format ''
plot x
plot x**2
plot x**3
plot x**4
unset multiplot

If you want to set absolute positions of each border, this becomes more cumbersome, because you have to set four margins for each plot (the layout options doesn't have any effect in this case):
set multiplot
set lmargin at screen 0.1
set rmargin at screen 0.47
set tmargin at screen 0.97
set bmargin at screen 0.6
plot x
...
Gnuplot version 5 offers a quite flexible way to produce equal rectangles, see my answer to Removing blank gap in gnuplot multiplot