Hi,
For your questions 1 through 3, I assume you are still looking at laminate based strain analyses and not ply based analyses.
1. The best way to get this type of information for now is the go to the sizing form | Options menu and turn on the flag "Generate More Detailed Reports...". Then analyze your component and when the analysis is complete, go to Options | Material and Analysis Detail. You should be able to find the margins of safety in each of the four directions. The intent is to fold this detail into the stress reports, however as of now, that detail is not included.
2. When doing the laminate based analysis, HyperSizer does not look at every ply. It looks at the outer surface of the outer ply of the laminate and the inner surface of the inner ply. There is no distinction between bending strains and in-plane strains. The strains used in the laminate based analyses are the total combined bending plus in-plane strain.
3. I believe what you are asking about is an interaction criterion. For example, Tsai-Hill or something like that. The laminate based analysis does not include an interaction criteria. To use interaction criteria, you must use ply based analyses.
For question 4, this is applicable to either laminate based or ply based analysis.
When you put in different temperatures on the material form, you are not telling HyperSizer to analyze at those different temperatures, you are defining how the material properties vary with temperature. By default, HyperSizer analyzes assuming RTD properties at 72 F.
If you want to analyze at different temperatures, you must create a thermal load set. If you are using a FEM, see the Pro User manual, finite element reference to create a thermal load set. If using a workspace, on the FBD tab, for each mechanical condition, click the "Thermal Load Set" radio button and then you can enter a temperature for the analysis.