Is the ODS (on disk structure) of the Windows server compatible with the ODS used by the Linux server?
Short answer: Yes, if they run on the same hardware.
The ODS structure depends on the CPU architecture. Today we have little-endian (Intel and compatibles) and big-endian (PowerPC) systems in 32 and 64bit variants. If you create a database file on 32bit Intel Windows, and then copy the file to 32bit Intel Linux machine, it should run out of the box. A good example of this is dual-boot environment where the database is stored on FAT32 filesystem.
Please note that simple copying of the database file is not a preferred method of moving databases around. You should backup the database on the source machine and restore it on the target - this way even incompatible systems (Intel vs PPC) will be able to use the same database. If you still decide to copy the database file, make sure nobody is connected to it. The safest thing is to turn off the Firebird server if possible. If you use SuperServer that's rather easy, but if you use Classic you should either disable the (x)inetd service for Classic (using chkconfig or other appropriate tool) or stop the xinetd itself. On Linux it's easy to check whether some process is using the file with 'fuser' or 'lsof' commands.