For a map:
https://ggwash.org/images/made/images/posts/_resized/image1_1_1020_1320_90.jpeg
Would seem logical to extend the WMATA line to Andrews AFB and make the transition from Metro to light rail there. Would seem like a good idea to extend the WMATA line to Andrews with or without the Southern Maryland Light Rail.
As to wire height: Other than when involving the railroad, the wire should be 16 feet above the track, or thereabouts. Where on the railroad, the wire should be 23 feet above the track or thereabouts.
The whole issue of wire height and offsets can be solved in the pantograph and arms supporting it. The arms supporting the pantograph contact bar would need to be longer in order to reach 7 feet higher. Can be done. The contact bar itself should probably be longer as well with the additional length based on the assumed angle of sway of the car plus deviation in cross level in the track. Again, no biggie. Calculate out what is needed and do it. The whole arrangement will be somewhat heavier, hence need stouter springs. again, can be done.
Consideration needs to be made for required offset from the railroad to platforms. Again, this has been done elsewhere.
Without reading the whole report (I don't hate myself that much), one question is how much street running, if any. This can have an effect on wheel wear and even the preferred wheel profile. As close to none, the better.
The "temporal" or in less fancy words limitations on operating times of the railroad and transit so as to maintain time separation can easily be handled. Assuming this is a one train or so a day branch the easiest is to have the freight outside the normal transit times with the transit system defining the times. If there is a need to run a train during the transit operating time, then this could probably be done by providing a gap in transit car times for the trains with the train setting there waiting its turn, not with a "hey we are going to have a train through here sometime or other" from the railroad. It is usually better that the transit system own the railroad. This piece of track should be upgraded for comfort of the transit passengers, but with tie spacing and rail, and structures if any, based on freight railroad axle loadings, which would probably mean closer tie spacing and possibly heavier rail that the rest of the transit system.
Track centers: If there will be two tracks on the railroad portion, track centers should be 20 feet, possibly 22 feet to provide required railroad clearance with poles between the tracks. If it is decided to use outside poles, meaning one on each side of the section, then centers can be 14 to 16 feet.
There are no insurmountable problems or even significant difficulties with this project when it comes to light rail and freight on the same track.