Just to clarify, a variant of padded order-based coloring called epobc is already implemented in coloredcoinlib (which is used by ngcccbase/ChromaWallet). It isn't document yet, however.

The idea is to use the otherwise unused nSequence field of first input to specify padding and differentiate between genesis and transfer transactions.

Padding can be chosen for each transaction individually and can be set to zero. 

Python code is here (I recommend waiting for documentation, though):  

https://github.com/bitcoinx/ngcccbase/blob/master/coloredcoinlib/colordef.py#L262

It is able to work with transactions with multiple colored and uncolored outputs, particularly, p2ptrade transactions.

Examples of p2ptrade transactions on mainnet:

https://blockchain.info/tx/f85b6213939c9cbc14538dd24838061179cac2485f50be20a974b819a85e5ee9 (It looks quite a bit weird, I know.)