The latest Kill Team rules can be found here:
http://www.games-workshop.com/MEDIA_CustomProductCatalog/m3460063a_Kill_Team_Rules_Pack_2013.4.pdf It really is going to come down to what each individual person believes the word 'combined Armour Value' means. One side will state you take the Armour values, including war gear that modifies said Armour value, to get the combined total. The other side will simply state that the combined Armour value is simply adding what is in the stat line of the model itself. They may even point to the rest of the rule which states (Side Front and Rear combined) as justification as to why war-gear that grants a temporary bonus is not included. Because the debate can exist, this is something you should discuss before the game so everyone is in agreement as to what this and other limitations in the same section mean.
Personally:
I think the limitation is only on the army list creation process itself and should
not take into account anything that might changes the numbers during the course of the game. This is because some legal action during the course of the game shouldn't magically turn a 'legal army' into an 'illegal army' and get you disqualified. The only way to prevent such occurrences, of perfectly legal actions disqualifying a player, is if you limit the scope of these rules to just the creation of the army and ignore them after the game itself begins. Therfore; as long as the model has a stat-line that falls within these rules, it should not be suddenly 'illegal' if an action or piece of war-gear suddenly changes the stat line during game play.
An example of another model which has war-gear that changes a stat-line to something 'illegal' during play:
One of the rules is models can not have a 2+ save, not a 2+ Armour save but simply a 2+ save. It is perfectly legal for me to take a stealth team because the best save it has is worse then 2+ but they have war-gear which grants special abilities that modify saves. It is also perfectly legal for me to move a model into cover, which is present as the mission statement states the table is 'generously covered in terrain.' So why then would me doing two perfectly legal things, moving a legal model into legal cover, suddenly get me disqualified for having a 2+ save?
If you think Stealth teams should be disqualified simply because they have a chance of getting 2+ saves:
Night fighting rules exist in kill teams and it would be very easy for
any model to gain the shrouded special rule while standing behind a ruin wall, granting a 2+ cover save....
in closing, also too long and didn't read version: Ghost arks have a stat-line that is legal and shouldn't be disqualified simply because a piece of war-gear changes this stat-line during the course of the game. The war-gear in question does have limitations which prevent it from being 'always in effect,' meaning that it only modifies the stat-line during certain situations. Now those situations are quite numerous, enough that you should avoid it in a friendly game simply because it is cheesy, but they are still not permanent changes to this stat-line and do not take effect till after the game has started. Therefore the Ghost Ark has not broken any of the 'at creation rules.'
The only way to disqualify it would be to also disqualify any other unit capable of breaking one of these 'at creation rules' during the course of the game, which I have proven is every model in the game.
Now I do agree the Ghost Ark is still a little broken but Kill Teams where designed to function at 200 points for a reason. At 200 points the ghost ark and a unit of troops, needed to purchase it in the first place, ensure the only model of note is the Ghost ark itself, with only half a dozen light infantry to support it at best. One of the key elements to Kill Teams is that numbers matter a lot more then they do in other
40K game modes, and a ghost ark sacrifices numbers for one heavily defensible model. Yet it is still a single model that could be brought low by superior fire-power of a much larger and better equipped army, particularly seeing you can have and should have at least one 'anti-vehicle' specialist with Lance or Tank Hunter to greatly increase the odds of killing such models.
This leads to the 'eggs in one basket' situation that would lead to the Necron player losing the tournament....