Well, you probably are required to file a tax return, believe it or not.
I think the reason you were rejected was that Married filing Separately needs to report any income over $5. So almost all people in that situation would have to file a full tax return with details about their income and sources.
So once you decide that you will be filing separately, you will be required to file a tax return. Or once your spouse files as separate, you are required to do so as well, and then are required to file a full tax return. There isn't much of a real-world possibility of a Married filing Separately who is not required to file.
I think that since very few people make less than $5 per year, by default your registration is rejected (the stimulus registration is actually just a simplified tax return). Or maybe it's a bug in the system, since there are some people who do not make $5 per year, yet the system is not allowing any simplified stimulus registration via e-file for married filing separately. So it's a little funny, that there is an option for filing separately, yet all will be rejected.
I think you need to file a full tax return. This would be even in the case that you do not make $5 per year, because of this bug. You should be able to E-file that way.
