I think you are misunderstanding how it all works...

To designate a ship as a 'flagship', it is just a passive ability.
If you have the Flagship gamemode activated, then loosing ALL of your flagships is game over, not just loosing one. The thing is, you usually only have one Flagship and can't build more (they're spawed as part of the victory condition) but if you make it possible to build more flagships, then all must be destroyed to trigger the lose condition.

They don't count towards the capital crew limit, because in the code they're classified the same as a Frigate/Cruiser (ie: a Frigate)

I think you mean the research files, but yes. Very easy to mod without doing anything with flagships.

I'd point out some key differences between flagships and capital ships...

First, as stated earlier, flag ships are considered frigates and so when it comes to ability filters, they may be targeted by abilities that can't target capital ships....

Second, there are specific technologies that affect capital ships but won't affect frigates (and therefore flagships)...for example, the Vasari have techs that cause capital ships to generate tax income and count as home worlds for victory purposes...

Third, any frigate that has the ability to bomb planets will always immediately go bomb the planet when under the control of the AI...this is not, however, true for capital ships and titans...

Fourth, capital ships gain XP which allows you to change the power curve in regards to abilities and stats....frigates are unaffected by XP, meaning the only way to modify how such ships progress through abilities or stats is through technologies...

In other words, it is not easy to simply replace capital ships with "flagships" unless you are willing to make some significant sacrifices or do some intense buff creations to link capital ships to "dummy" flagships...

Hi Wintercross, 

Could you explain how you created a starbase as flagship? A while back I tried it but while the game accepted frigates, capitals and titans as flagship it crashed when I tried to set a starbase as flagship.