Rogue/Ninja Starting Class?

[JakzChurchill]

or B: Yugiri had to make believe she knew nothing of the Rogue battle style or it would show they had been spying on Eorzea.

all this part will retcon all that was said in the 2.1 and 2.2 story line. Yugiri clearly states that she will take care of the dojo and secondary she is really surprise to see a similar fighting style that how thancred have open up about the thief guild.

You either didn't read that at all or chose to ignore it. Both instances i laid out clearly explained Yugiris actions, either she wasn't involved and really didn't know about the Rogue guild, or she knew but had to act like she didn't as to not allow the Eorzeans to find out they had been spied on, ruining negotiations with Eorzea.

And I'm pretty damn sure they would have some spies lurking around, the nation practices Ninjitsu, a fighting style specifically designed for scouting and stealth missions. Any information that could be gathered whether on the Garleans or on neighbouring nations would be of use to the Domans in any battle. Especially the fact that the scouts in the doman army would be trained as scouts and wouldn't be of much use on the frontlines, instead they would be sent out to gather in information they can to help the main battle regiment.

EDIT: Should also add on the point about her setting up the dojo, this may not mean we will make use of that dojo, the Rogue guild is already established so you will get your class there. But every other job has involved talking to one person, not a guild leader, usually an individual who has some connection to the job you are learning. This could mean we use a different doman to get the job information and Yugiri could be busy teaching the general public her fighting style.

Maybe she doesn't even teach any Ninjitsu, and we learn this from our secondary source, giving us an ability to set us apart from those taught at the dojo.