The -5 fellowship and +5 agility are the result of a special ability you gain in stage 4 of character creation; nor does the ability specifically state you replace your chapter characteristic modifiers (which occurs in Stage 2 of character creation) with these. You can only select advanced specialities in, or after, Stage 4 since you must be able to spend XP in order to purchase the advanced speciality (Stage 4 is when you're first allowed to spend XP).
The XP cost (200) is deducted from your starting XP (1000) since you are purchasing the specialty with your starting XP. Thus a newly created Wolf Scout has only 800xp remaining to spend after purchasing his advanced speciality.
The Tactical Marine speciality (which you must select in Stage 3 of character creation to be eligable for Wolf Scout) begins the game with Command Trained. The Wolf Scout trades this for Shadowing Trained.
The difference between trained and untrained is (just in case):
Untrained Basic skill: Can test, but at 1/2 skill's characteristic (modifiers are not halved)
Trained Basic skill: Test at skill's full characteristic
Untrained Advance skill: Can NOT test at all, any forced tests auto-fail.
Trained Advance skill: Test at skill's full characteristic
Command is a Basic skill for Astartes. If Untrained you can still use the skill, but at only 1/2 of your Fellowship characteristic.
Shadowing is an Advanced skill, you can ONLY use this skill if Trained.