I can give an example of what the OP is talking about.  Think of a colored coin or Counterparty asset that represents USD.  It is built on top of the Bitcoin blockchain, and can transfer USD$1,000,000 as a 0.0001 BTC token.  The only problem, and this may be a big one, is in securing this transaction.  The Bitcoin network sees this as the sending of 0.0001 BTC, nothing more.  It's the colored coin or Counterparty layer on top of Bitcoin that interprets it as something more.  So any security features that rely on amount of Bitcoin being sent, such as how many confirmations to wait for, will be rendered unsafe.  Your seemingly small 0.0001 BTC transfer may have needed only 0 or 1 confirmations, but the fact that it actually represents USD$1,000,000 means it would be well worth the effort to perform a double spend with so few confirmations.

To summarize, you run the risk of having less security when you override the meaning of a BTC transaction.