It is a little more complicated than that. Even though the Blue UberGROM boards have a flash chip in them, it is not possible to flash them in system--you have to do that in an EPROM burner. The second important thing to know about the 512K of flash in the UberGROM is that it is bank-switched ROM. TI cartridges have always been a mix of ROM-only (most of the third-party cartridges), GROM only (mostly TI cartridges), or cartridges with both GROM and ROM on them (mostly TI cartridges). The flash chip uses the same bank-switching system TI did (from the software standpoint), but significantly extended. TI used a maximum of four banks, the 512K Flash chip uses 64 banks.
In addition to the flash chip on the UberGROM board, you can install an ATMEL 1284P. Using the initialization code Tursi created for that, this chip is now capable of emulating up to 120K of GROM and 12K of GRAM. The GPL programs in the various 8K GROM slots CAN be reprogrammed in system using his loader software--but note, this is for GPL programs, not Assembly programs. These programs may also use ROM code (programmed into the 512K flash chip), creating the same style of hybrid programs TI did back in the day.
The capabilities of the cartridge thus allow it to reproduce any cartridge ever designed for the TI with the exception of the MBX cartridges, which also required 1K of on-board RAM. It also allows distribution of completely new software designed to take advantage of its expanded capabilities.
For development, the entire cartridge is emulated in the CLASSIC99 emulator, so it is possible to build and test new software in a PC environment and only transfer it to a physical cartridge once development is complete. There are many development tool sets available on the PC side. Read through the Developmental Tools thread to see which items are best suited to the way you program.
Also note: Black, RED, and Yellow boards use standard EPROMs of various sizes, and are excellent choices for ROM-only cartridge programs. They are also emulated in CLASSIC99. Black boards use Type 3 cartridge images, Red, Yellow, and Blue UberGROM boards (for the 512K flash) use Type 8 images.