Re-writing a large project from scratch is often much harder than it looks like at first. Chances are if the code is a mess then the requirements and documentation are in even worse shape. You are going to be spending a lot of time coming up with requirements and figuring out how and why each part of the spaghetti code works. You are going to be constantly asking is this particular behavior a bug, a feature, or merely a convenience for the guy that wrote it.
From your managers perspective and hopefully from yours as well the ultimate goal is to create value for the business. After all as a professional we don't write code just to write code we write code in order to make money.
Something that you may not be looking at is the level of risk for the company and for your manager. If you start working on building from scratch and are not able to complete it for whatever reason the new half completed re-write could end up abandoned. Think of where this re-write would be in terms of priority if there is already a working version and the primary architect leaves in the middle of the project. Would there be a strong enough reason for the company with this upgrade?
Compare that to refactoring the existing code where there is still an actively developed version of the project. If you are no longer available to work on the project it won't be ideal but the risk is much lower.
For a manager to let you do a complete rewrite takes a lot of trust and is only occasionally worth doing even though rewriting is way more fun than cleaning up some one else's mess.