I believe they are probably gonna work out a better way at some point. Think about how broken it would be to trade mats for marks and marks for mats. There would be balancing issues that would cause one side or the other to find it useless. Since you trade 10 Marks for 40 Mats it is obvious they intended for it to work side by side considering 50 mats got you 10 marks. Although I'm sure they found something that caused it to not work at this point in time.
Hopefully they fix it by just making Vanguard marks allowable to spend on factions. Only reason they wouldn't is because that would break the 100 mark limit and you could practically armor up in one week if you dedicated to both PvP and PvE. Which in the end is a lot of dedication and wouldn't necessarily "break" the game but make you level up much faster then anticipated upon reaching level 20.
Edit: In no way do I disagree with you, I believe there should be many options for gaining marks and faction rewards other than grinding PvP. Not everyone is as skilled as the next and PvP shouldn't be a forced option when playing the game.
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Its ten marks for twenty mats.
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Thanks, I never exchanged mats so I was making a guess. Although now I can see how this would create an endless loop of exchange if they left it, as is. I'm guessing they'll reintroduce it at some point with a difference in values.