Rav Yosef Shalom Elyashiv (contemporary) records the practice of the "Medakdekim" (those who are especially meticulous in their Halachic observance) not to rely on any Kashrut certification of Masot, and instead eat on Pesah only Masot that they baked personally (listen to audio recording for precise citation). He ruled that it is therefore preferable for people to form groups that bake Masot and personally oversee the entire process, including cleaning the utensils, to make sure that the Masot were baked properly. The reason for this custom is that Masa is the product that can most easily become Hametz. Therefore, it is worthwhile for communities to form Haburot (groups) to bake Masa themselves, rather than rely on the industrial manufacturers, even those with valid Kashrut supervision, given the mistakes that could occur in the industrial manufacturing process. This would certainly be an advisable practice for synagogues, to go as a group to a Masa factory several months before Pesah to bake the Masot that they then eat on Pesah.
The Mishna Berura (459:10) writes that those baking Masot must work especially rapidly when placing the Masot into the oven. The area right outside the oven is, of course, very hot, and the intense heat could cause the dough to ferment and become Hametz before the Masa has a chance to bake. It is therefore critical not to delay at all near the oven, and to place the Masa from the stick into the oven immediately.
A question was once brought to Rav Elyashiv concerning a bakery where one Masa was held on the stick for several moments before being put down in the oven, while the baker searched for a suitable spot inside the oven. This Masa was later mixed with the other Masot in that batch, and the question arose whether perhaps the entire batch should be deemed unsuitable, given the possibility that the Masa in question had become Hametz due to the delay in placing it inside the oven. Rav Elyashiv ruled leniently, noting that we may rely on the possibility that the Masa had already begun to bake inside the oven, and thus did not have a chance to become Hametz. In any event, the fact that the question was raised demonstrates the importance of working rapidly during the process of placing the Masot into the oven.
Rav Elyashiv ruled that when possible, each stick used for placing Masot into the oven should be used only once. The stick absorbs some of the dough, and that dough may become Hametz inside the wood of the stick and then affect the Masot that are placed upon it subsequently. This is a measure of stringency that may not be feasible in an industrial system, and this is yet another reason why it is preferable, for this who are able, to bake their own Masot, as they are able to maintain the highest standards, which are not always practical in large-scale production.
The custom is to examine each Masa that comes out of the oven and discard any "Masa Kefula," meaning, a Masa that has folded over, and is not perfectly flat. The concern is that the dough in the folded area was not fully baked and thus became Hametz, and therefore any "Masa Kefula" is broken and then put to the side and considered Hametz. Rav Elyashiv ruled that if a "Masa Kefula" had been placed on top of another Masa, the Masa on the bottom is permissible for use on Pesah. We do not have to go so far as to suspect that the bottom Masa became Hametz from the top Masa.
Summary: It is worthwhile, when possible, to bake one’s own Masot for Pesah, rather than rely on the supervision of Masa factories. When one bakes Masa, he must ensure not to allow the Masot to stand still for even a moment right near the oven; they must be placed from the stick into the oven immediately, without any delay whatsoever. It is customary to discard Masot that doubled over during baking, and are not perfectly flat. The Masot that were underneath such a Masa are permissible for Pesah.