I don't think there is a single answer for your question because there are a few factors that determine how you'd approach a quote or proposal.
Although very rare, if a client has a reasonable grasp and documentation or the project is a very simple one you can usually provide a good estimate to the client. But as everyone knows that's a rarity and scope creep has to be factored in to your cost projects.
In this case the time required for you to prepare the estimate/proposal should be much less than if you have to determine the requirements list and scope of changes. So I'd consider this type of quote the 'cost of doing business'. Unless your quote falls under the LOD caveat below.
You also need to clearly define what is and what is not covered in your original estimate as well as the rate and billing terms of change requests. Obviously there will be some back and forth with the client when these things come up, but a well written proposal/quote gives you something in writing to fall back on in your argument.
Level of Detail of the Proposal
How much detail are you providing the client in your proposal? If you're spelling out anything other than the 40k foot overview you're providing the client with a blueprint of the project requirements. In this case you're putting a great deal of effort and man hours in to your proposal which the client can simply hand to the lowest bidder.
You've done a great deal of the work without any benefit or payment for your services. So charging your customer for the consultation would be perfectly reasonable.
Many clients will balk at this, but I've found that if I tell a client that the estimate is X dollars up front but I'll apply that to the cost of the project if I'm selected they don't seem to have an objection. Obviously you'd need to factor that in to your total project cost so that you're not losing anything.