I think flag order could be ignored when other factors might come into play with later releases.
Code Red has said in that DEV journal entry with that hella cool looking insurgency map that assets and flags being linked is something that is gonna become more central to how PRs flag capping works, hopefully it will become more common too.
So you could have a map where all flags were cappable but the asset bonuses wouldn't come into play if you didn't have certain flags.
Allow me to demonstrate on this badly illustrated map using everyone's 2nd favourite "Wow! That's alot of assets!" map;
This is the AAS system, but say it didn't apply to flags, just assets so this kinda thing could happen...
So you could take a flag if you thought it was a good tactical decision, but you wouldn't benefit in terms of gained assets, so you can weigh up the pros and cons of both approaches and what kinda game you wanna play.