If you have 6 28 pin ROMs, then you may read them as 27C256 EPROMs. Only 1 Mbit ROMs had different pinout than EPROMs, 256 kbit ROMs are pin compatible with EPROMs (as for reading of course). Reading does not require any vendor specific conditions, so you may choose any IC manufacturer you want.
For 2 ROM machine, you could easily replace them with 27C1000, or with some more hassle with 27C010.27C1001.
For switching from 2 to 6 EPROMs you need to change some jumpers/bridges. Changing from 6 to 2 usually requires adding one IC.
Atari branded ROMs could be either Mask-ROMs or OTP EPROMs actually. Mask-ROMs are very unlikely to fail.