Are the transactions in use with swapbill actually accepted by the major bitcoin pools? I know a lot of non-standard transactions are simply not mined for safety purposes.
The current encoding from SwapBill transaction to raw Bitcoin transaction is very straightforward, doesn't require any non-standard features, and there shouldn't be any issues with either network relaying or mining of these transactions.
You can see the actual code for this
here, in the Create() function.
(btw. The flip side of this is that this creates unspendable outputs.
It would be nicer to encode the transactions with OP_RETURN and avoid unspendable outputs, but last time I checked this wasn't considered standard by litecoind.
Changing the transaction encoding to use OP_RETURN is not hard, and doesn't affect the rest of the protocol.)