Soaking time for your wooden, or weed, tree armatures will depend on just how dry they are before you start. If they were found lying on the ground after a long spell of dry weather they are probably well dried out. However, if they were broken off living trees, or plants of some type, they are likely to still be quite green and won't absorb the Matte Medium. That's OK, as the coating will simply seal in the existing moisture. So...a 1 or 2 minute dip in Matte Medium for the really dry stuff, 15 to 30 seconds for the fresh, and you should be fine. Let the dipped "trees" dry AT LEAST 24 hours in a warm, dry, location with good air circulation.
For other purposes, I consider Matte Medium as THE universal bonding agent for groundcover and have used it almost exclusively for years over my entire layout in scenicking. However, for this application it needs to be treated a bit differently. You should dilute the Matte Medium 1:4, or even 1:5, with water in a large container (quart or gallon milk jug) and shake well. Then set aside for a day, or so.
Matte Medium gets its flatness, or matte, appearance from talc. If the liquid is used immediately after mixing it can dry leaving a whitish film. This you want to avoid. So allow the mixture to settle and draw your bonding liquid only from the upper, or top, 75% of the container. Used liberally, this liquid will give you a perfectly invisible, but very strong bond for all your groundcover, ballast, etc.
Below is an example of the sort of results I've gotten using Matte Medium as a scenery-bonding agent.
NYW&B