happy to help. The question you're asking here concerns a massive chunk of biology so theres a tremendous amount to learn. If you want to learn more, the key is to take it in bite sized chunks and go at your own pace. To start, you could look at a simple case and search "explanation of the lac operon" which was one of the first systems in which gene regulation was well studied, or you could just search the term "gene regulation". Alternatively any biology textbook will have tons of information on gene regulation, even the slightly out of date ones. Finally you can check out the book "Endless Forms Most Beautiful" for a slightly lighter read, written by an expert in the field and a great science communicator. This last option might be the most enjoyable because of the digestible writing style compared to a textbook.

Yes but the result would be a little boring. It would without doubt create a nonviable organism.

The reason is that DNA contains critical regions outside of the protein coding part. These include promoters, repressors, enhancers, and numerous RNA transcripts that serve a wide array of functions. Divorcing the part of the DNA that codes for a protein from all the other parts that regulate the expression of that gene would result in dysregulated expression and would certainly be lethal if applied to all genes simultaneously.

Yes and no, separation is an important part of keeping microbes out of areas where they can cause damage however the immune system regulates all microbes to some extent and recognizes them based on a variety of factors but some have a privileged status. This isn't really my area but commensal microbes engage in crosstalk with the immune system which is necessary for long term colonization.

Here's an article with more information: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4109969/