Re: libero SoC v11.8 is not showing all the tool options
I use 11.8 Silver (free) for Igloo's and I've never seen those lines in Design Flow, and you have some I don't see. I suspect it depends on the part and the license level which you didn't see fit to reveal.
11.8 is pretty old but I have to use it because 12.x doesn't support Igloo. But if you are using a newer part, maybe you could try a newer version of Libero.
In any case, this sounds like an issue that needs Microchip support rather than this user forum. I suggest you submit a support ticket.