Translation:I eat breakfast.
Different tense, different meaning.
"食べます" is the conjugation for the polite present indicative, similar to the simple present tense in English. This tense indicates either a habitual action, or statement of fact, and the action may or may not be happening right at that very moment. It is akin to saying "I dance salsa", or "the sun rises in the east". It is a thing that happens, but it's not necessarily something that's happening right NOW. This same conjugation in Japanese is also used for the simple future tense in English, so you could also translate this to "I will eat". You'll have to rely on context to determine which it should be.
"I AM EATING breakfast" in both English and Japanese is known as the present progressive tense. It indicates an action that's in progress at the time of speaking. For that tense in Japanese, you'd be using the conjugation 食べています.
を is used to tell that the phrase before it was an object, meaning someone is doing something to it. In this case, someone is eating the breakfast, the breakfast is not doing the eating. In English we use special forms of some words to show that they are an object: him instead of he, her instead of she.
Well, @JelisW already provided a pretty good explanation of this difference earlier on this page.
They pointed out that 食べます can indicate future tense. In English, "I am eating lunch (later)" can also be future tense, although "I am eating lunch" is much more commonly associated with present progressive tense, which uses a different verb form in Japanese.
To address OP's question, 「あさごはんを食べます」and「おひるごはんを食べます」 can both be translated as "I eat breakfast/lunch" OR "I am eating breakfast/lunch (later, i.e. "I will eat breakfast/lunch")" depending on the context. However, I suspect that allowing, or even correcting to, "I am eating breakfast/lunch" is a developer oversight which should be removed, as it (evidently) just causes unnecessary confusion at this stage, despite being technically correct.
The "command" or imperative form of a verb in Japanese is very different from the present/non-past form that we have here. There are different ways to conjugate a verb into an imperative form, depending on the type of verb and the level of politeness you need, but I'll give you 食べなさい as the polite yet stern command form of 食べます.
The subject (in this case, also the topic) is omitted because that's what Japanese people do when it's obvious through context. We don't have any context to go off of, so it's safe to assume that the person speaking is speaking about themselves.
The conjugation is 「食べています」or「食べている」, and it is used to convey that the action of "eating" is currently being done.
The normal 「食べます」 conjugation is used to convey that the action of "eating" is generally/habitually done or will happen in the future. These two conjugations don't overlap in terms of usage.
Where you might be getting confused is the fact that "I'm eating breakfast" in English can be used to convey that the action of "eating" is currently being done or it will happen in the future (e.g. "I'm eating breakfast with my friend tomorrow", obviously not currently happening but still natural, albeit colloquial, English). Which conjugation you choose in your Japanese translation therefore depends on the context of your English sentence. But when you're going from the Japanese to English, 食べます means "I eat" or "I will eat" depending on the context, but never "I am (currently) eating"
True, but as said in other threads, this is because the individual dynamic speech synthesis does not take into account the whole sentence instead of units; the same goes for the readings of kanji, you often get some native Japanese reading when another (a Sino-Japanese one, for instance) is expected.