What is the ruling on someone who said: "If my prayer were presented before Allah, it would be...", then doubted whether his statement indicates a doubt that prayer might not be presented to Allah, despite his certainty that all deeds are seen by Allah and presented to Him?

The statement you mentioned might be intended by its speaker to convey a correct meaning, such as Allah's awareness of deeds at specific times, and this does not negate His comprehensive knowledge of all the states of His creation. As long as the speaker is certain that Allah is aware of everything, then a fleeting doubt has no effect, because certainty is not removed by doubt. However, if it is merely a passing thought, it has no ruling unless the heart settles upon it, according to the Prophet, peace and blessings be upon him: "Indeed, Allah has forgiven my Ummah for whatever thoughts they harbor, as long as they do not act upon them or speak of them." It appears that this doubt is caused by whisperings (waswasah).