First of all the chumra of two kzaysim is only on the baal haseder. The reason is the bracha of hamotzi and the achilas matza each require their own kzayis. The biur halacha 475 dh kezayis is mefakfeik in this chumra and the chazon ish himself was not makpid on his shiur for these two kezeisim, rather he was somech on the shitos that our kzeisim is enough.
About taking matzaa from the box- it should be noted there is a big machlokes if you need a kzayis davka from the middle matza or if you can take a piece of the middle matza and eaat a kzayis of another matza. Reb Shlomo Zalman in HAlichos shlomo says you can be metzareif from other matzos. However, the brisker rov held since one of the definitions of lechem oni ?????? ???? ????? ???? which is the hagada the matzos should be on the table during maggid.
About the chumra of kdei achilas pras, while pashtus you are right that the two shitos don’t make sense the steipler in shiuron shel torah says to be makpid on 2 minutes lchatchilah. Probably, the reasoning is kdei achilas pras is a set time based on eating pas lechem not on matza. ( however lfi this it must be six times quicker to eat lechem)