IF you've patched the GPU bios with Atom15 set to 15kHz-only, and flashed it to the card, then that card's bios is only capable of outputting 15kHz during boot. When Windows takes over, crt_emudriver will deliver 15kHz as well. How it delivers these modes means that even though your desktop and all installed resolutions are stable, you might get a flickover screen that jumps vertically while Windows loads. But it only lasts for a fraction of a second, and should not be a problem.
The only thing to look out for is how sensitive the Sanyo 20EZ chassis is. If it can handle a standard arcade range of about 15.5 to 16.2 kHz happily, then you should be fine.