If i am not mistaken, and i can be, im at school and not close to the game to check the files, but "phasecloak" on the phasescout (frigate) "does" allow movement while phased out, the purpose of "phaseout" i believe, and i am guessing here at the intentions of the devs, but i see it as phaseout is a combat ability that "evens" the sides, phase out is used both against the enemy and against friendly ships. The enemy ships of course are disabled and cannot run or fire, which save the home fleet some time to recuperate in heavy battles, or if they are outnumbered.
The friendly ships that are affected by phaseout are saved some damage by becoming momentarily invulnerable, but doesnt allow them a larger margin of favor by allowing them movement or the ability to phase jump. So it is fair to both sides, offering no advantages to one over the other.
By phasecloak being able to move while phase shifted, being an ability used by scouts, which are mostly, not always of course, but mostly planet observing travelers, the phase cloak allows fairly weak scout ships to survive a few minutes longer in hostile gravity wells than they would otherwise. It is a "self only" ability in that it offers a little more protection for the scout, but doesnt affect the enemy ships at all. In this way, it probably is considered a "scout skill" not a combat skill. And while phaseout could be said to be a combat skill, it is mostly a shield ability for the friendly ships, or a "momentary stop" ability against the enemy, not aggressive at all, especially since it makes the ships, both enemy and friendly invulnerable to attack for a short time.
Anyway, with regards to having the phase out accomplish by itself what the disablephasejump, disablelinearengines and disableangularengines does separately, i cannot exactly say, other than guess that perhaps those values going into the game engine are read and and when expired they cancel those same modifiers. I am guessing at this point that simply having phaseout listed alone may possibly produce an error, or may not correctly re-start the engines when the ability expires.
Also, as the gentleman above stated, it may simply be a way of the devs insuring that the ships affected are not targeted. The means that the game uses to target ships may need those modifiers specifically to ignore them.
Anyway, these are my ideas of why phaseout, and phasecloak and the modifiers are used. Absolute clarity of course can come from asking the Devs, who will not "guess" as i have done, but be able to tell you exactly why they did it. 
Take care and Keep Modding!!!!!
-Teal
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