subway and minyan

Question

1) The commercials for subway advertise that they bake cheese into some of their breads, their new special item. Could this pose a problem, lets say, if this bread is baked in the same oven as the cheeseless bread? 2) In order to fulfill tefilla betzibbur, does one have to start with the minyan, or can he simply join in the middle. This has many practicle applications, namely, how much of pesukei dzimra one should skip, and whether he should take his time during shema if it means that he won't be able to start shemoneh esrei with the chazzan. Thanks for the reply!