1) The file format is the same, but you do need to review layouts by opening the files on both systems to check to make sure that it displays properly on both. Windows systems require a bit more horizontal and vertical space to display text of the same size and font so a layout designed on a Mac often needs a few adjustments to display correctly on windows. Also, you need to make sure that the same fonts are installed on both systems.
You need to install the Mac application on the Mac and the windows application on windows, you can't use the same application on both.
2) There are several options for restricting access to your database file. You can set up passwords such that they do not have access to the design of your database without the use of a password that you do not give to them. You can still make it possible for them to add new passwords and specify privilege sets if you design a layout and add scripts, set to run with full access permissions that allow them to change passwords and add accounts.
You can also use FileMaker Advanced to remove the full access account from the copy of the file that you distribute to others. (You keep a different copy of the file that still has this account so that you can continue to make new changes to the design of your file.)