The fundamental difference between W-2 and 1099 isn;t based on travel expenses.
W-2 means that you are an employee. There is a "20 questions" rule that decides whether you are an employee or a independent business. If you worked on the employer's site, used their equipment and had hours and the manner in which you did the work determined by the employer, and if the employer had you working for a supervisor, then you were an employee. In that case it is illegal for you to be paid a 1099. If they force you to be a 1099, at the end of the job you can claim unemployment benefits, which means the state goes after them for the taxes. To dispute your status with the federal government, the last I knew, you have to file an SS8 form.
If you worked at home or in your own office space and did the work during the hours you chose and if the manner in which the work was determined by you, then you can quality as a 1099 independent business (possibly a sole proprietor). But this may mean extra taxes - self employment taxes because the employer didn't pay into your Social Security and Medicare. You might also have state B&O taxes and need a business license. It also means that you have to keep all your receipts and itemize deductions as fill out the profit and expenses form on your tax return.
Per diem vs. a profit and loss form is only a very minor part of 1099 vs. W-2. In a 1099 you are an independent vendor selling the client a product.
If you are forced by economic necessity to accept a 1099 status when you are really an employee, know that this could end up in a dispute. The employer may try to force you to sign a contract saying that you are not an employee. Try to avoid signing anything like that or cross it out when you return the contract and initial the crossing out and keep a copy, and even write that you don't accept that clause.
Of course if your goal is to own a business rather than being an employee, then take all the 1099s you want.
Here is another difference: In the 1099 world you are not on payroll, so there is a possibility they might not pay you or might delay in paying you. This can be true for small companies that are not selling enough product. Then you have to do collections. I had that experience and that is why I got out of the 1099 world a long time ago.
