You actually just described the facility that I work in to a tee, as we make RTE and Frozen products.
As for your first question, this is from the FSMA FAQ from the FDA:
"The preventive controls final rules require that a facility verify that hazards are being controlled and take corrective action to prevent contamination; and product testing and environmental monitoring are examples of steps a firm may take. A facility’s decision to conduct product testing, and to establish the frequency of such testing, will reflect a risk-based approach consistent with its hazard analysis. Consequently, the FDA expects that facilities that produce foods that have frequently been associated with outbreaks of foodborne illness or pathogen contamination, or produce ready-to-eat foods for which an effective preventive control cannot be implemented, would establish product testing programs more often than facilities that do not produce such foods."
"Similarly, a facility that identifies an environmental pathogen as a hazard requiring a preventive control, for example, sanitation controls, would conduct environmental monitoring. Such a facility would decide what, if any, role product testing would play as a verification activity or as part of a corrective action as a result of positive findings from environmental monitoring, based on the facility, the food, the nature of the preventive control, and the role of the preventive control in the facility’s food safety system. "
Given the language used here, I would say that Environmental Monitoring throughout the production and storage areas of the facility is necessary. The frequency of the swabs should be determined based on a solid risk analysis of each area.
I'm afraid that I can't be terribly helpful for your second question. We contract our microbial testing to an outside lab. I do know of a handful of facilities that have a microbiological lab on-site, but the lab tends to be in a separate building than the production floor (aka, still on 'factory' grounds, but in a separate structure). That said, I know of one lab where it is in the same building as production.