What about minimizing your window after creating it?
$ (mate-terminal --window-with-profile=Background --title=xxx  --command top >/dev/null 2>&1 &); sleep 0.1; xdotool windowminimize $(xdotool search --name xxx|head -1)
I use Mate instead of Gnome but it should work just the same if you replace mate-terminal with gnome-terminal:
$ (gnome-terminal --window-with-profile=Background --title=xxx  --command top >/dev/null 2>&1&); sleep 0.1; xdotool windowminimize $(xdotool search --name xxx|head -1)
First, i create new window with mate-terminal and I assign name using --title=xxx option. After that I use xdotool search --name xxx|head -1 to find id of this window and I pass it to xdotool windowminimize. sleep 0.1 delay is necessary because window needs a little while to be created.
Instead of using window title you can also use other search options:
$ xdotool search Usage: xdotool search [options] regexp_pattern
--class         check regexp_pattern agains the window class
--classname     check regexp_pattern agains the window classname
--maxdepth N    set search depth to N. Default is infinite.
                -1 also means infinite.
--onlyvisible   matches only windows currently visible
--pid PID       only show windows belonging to specific process
                Not supported by all X11 applications
--screen N      only search a specific screen. Default is all screens
--desktop N     only search a specific desktop number
--limit N       break search after N results
--name          check regexp_pattern agains the window name
--title         DEPRECATED. Same as --name.
--all           Require all conditions match a window. Default is --any
--any           Windows matching any condition will be reported
--sync          Wait until a search result is found.
-h, --help      show this help output
If none of --name, --classname, or --class are specified, the  defaults are: --name --classname --class
Example using --class 'mate-terminal' option:
(mate-terminal --command 'top' &) && sleep 0.1 && xdotool windowminimize $(xdotool search --class 'mate-terminal' |sort|tail -1)
This should work for gnome:
(gnome-terminal --command 'top' &) && sleep 0.1 && xdotool windowminimize $(xdotool search --class 'gnome-terminal' |sort|tail -1)
I sort output of xdotool search since newly created window should be last one listed.