There is no way to infer that Protoss lost their mouths and became photosynthetic from reading the manual. The only way to infer that Protoss are photosynthetic is by seeing their artwork, not reading the manual, and not knowing that photosynthesis is not practical for powering animal metabolisms.
It is physically impossible for animals like the Protoss to survive on photosynthesis. Even with 100% efficiency, which is physically impossible btw as the loss is due to metabolic processes and not just the limited absorption of light, they still do not have enough surface area to absorb enough energy from sunlight to power their metabolisms. Sunlight simply does not have enough energy density in that small a space.
However, if that is not sufficient to convince you, then I will use an explanation based solely on the lore.
Firstly, the xel'naga were not that advanced, as shown by the manual explicitly stating they were surprised by the Zerg's skill at genetic engineering. This would suggest that xel'naga were not capable of the same morphological alterations that zerg made. The zerg also gained the xel'naga's knowledge and skill by eating them. Since the zerg are canonically better genetic engineers than the xel'naga and have all their knowledge and skill, then it would stand to reason they would make themselves photosynthetic if it was a viable option. Since they have not, it stands to reason that the xel'naga were either not capable of this or that it is not viable to make that alteration. But you could argue that creep utilizes biological photovoltaic cells, since it is grey and has a huge surface area to catch sunlight.
Secondly, the photosynthesis retcon was part of the overall wimpifying of the Protoss. In the SC1 manual the protoss were nearly physically perfect and could survive in almost any environment stark naked, which was the original definition of purity of form. Shakuras was darker than Aiur, but the nerazim were so wimpy that they need to genetically alter themselves to survive on moonlight. In the DT novels they needed to wear animal skins to avoid freezing to death in
tropical jungles. Hardly pure of form, they are actually inferior to humans in every way.
Thirdly, protoss portraits breathe while idle and some of them wear gas masks. This would only make sense if they had lungs and breathed through their face, even though the Field Manual explains they have no lungs or orifices.
Fourthly, it is not like the art direction and lore has not been wildly inconsistent on many other occasions. The zealot in the SC1 Protoss mission success screen has a cone head, no apparent nerve cords, and freakishly long fingers. Compare that to the SCR artwork, which is supposed to represent the most recent conception of Protoss anatomy. Artanis varies wildly in appearance across the games and even within SCR his 3D model and 2D portrait look completely different. Zeratul has nipples only in some of his appearances, but not others.
Fifthly, the fluff constantly contradicts itself and just plain makes no sense much of the time. The Field Manual explicitly states that Protoss have no orifices whatsoever. Whatever definition of "orifice" it is using is suspect, since the Protoss have eye sockets would should qualify as orifices. The microscopic pores they supposedly use for eating/shitting should also qualify as orifices. The authorship is just scientifically illiterate despite supposedly being written by actual scientists.