Indexing, diskdefrag, vscan or backup of a filemaker file when users have it open CAN cause corruption.. not WILL but CAN.. important distinction.
Very good set of questions and I also like coherentkris' response... although a bit brief.
FileMaker Server has always been very forgiving and stable in my opinion. It's only weakness has been the java for the Admin Console and so long as you leap that hurdle it has usually been setup for the life of the server.
You are talking development machine... not production machine, I believe. In this case you be a lot more lax about those recommendations.
It is ok to run FMP on the same machine. You obviously can only run one of them as the host at the same time unless you change the hosting port... for FM Client or for Web publishing.
I have never partitioned a server... but I am planning it for my latest production server. I don't think I would go to that trouble for a development server.
I have always had single machine configurations with MacOSX Server as the companion Apache web server and have run full mail, calendar etc services on each as well as FMSA. I host many domains and have mostly full web interfaces to databases for public and member access and both web and FM CLient admin access. I also have Lasso and even some old CDML sites. All of this is robust in the Mac environment and the weak point is always the limitations on my bandwidth.
I have never turned off Spotlight. In fact I deploy it in some web sites where I allow file searching.
Some of the best assistance for a beginner comes from FMI's own materials supplied with the installs... including the documentation and the examples and the templates. The other essential is the FTS (FileMaker Training Series) which you can download for free (along with FMSA developer edition) if you paid your TechNet $99 membership.
Next the resources section of this TechNet site is comprehensive and there are some excellent white papers and how-tos.
Next... you look at the sites and blogs of the many developers who have published many wonderful documents and code collections and who provide freely downloadable unlocked databases as demonstrations. There are many and most can be found here but I suggest you search the "Consultants" section of the FMI web site then follow the links to their site to see what they are offering.
The beauty of the example and template databases is that you can de-construct them.Make sure you have the developer edition of FMP... FMPADVANCED. It will allow you to copy and past elements from one database to another.
The PHP API is as simple as any other API or class of PHP to learn.