I think this is a great misunderstanding. Initially there was a huge amount of Bitcoins raised and sent to the Exodus address to create something very innovative - the Master protocol. Those coins were and are used to pay for bounties and whatsoever and controlled by the Mastercoin Foundation - whose members are those with a high stake in this game (if I'm not mistaken). This means: coins in the Exodus wallet = funds for the project itself.

The output to the Exodus address is another thing: there are several ways to tag and identify a meta-transaction, for example transactions can be created with an additional output to a specific address (Master protocol) or one could encode some magic bytes (XCP) within the data payload. Or one may use OP_RETURN with some magic bytes etc. etc. ...

But there is actually another reason: DOS protection. DOS is not yet an issue and may not be in the short term, but for the same reason that there is a DEX fee (XCP and MSC both use one) or a Bitcoin transaction fee in general, this is a filter against spam.


Re MSC vs. XCP: both projects follow different approaches, for example:

Pre-funded by the community vs. ongoing funding by donations
Coins were bought by funding the project vs. proof-of-burn
Transaction marker is an output vs. marker is encoded within the data payload
An additional transaction processing fee is raised vs. no additional transaction processing fee
Many developers and different parsing engines vs. one implementation
Only sellers in the DEX orderbook vs. buyers and sellers
...

I wouldn't say one or the other is better or worse - each approach has benefits and downsides. In the end XCP is a MSC fork and because of this there are of course great similarities, but I hope over time more differences will emerge and I'm very curious where all this leads to.