1) VM's are not officially supported. Rumor is they work but since they are not supported we did not go that route. I would seriously consider this before you go that route.
2) Triads have gone in and out of favor. Flexera has made improvements in their support of triads in latest releases but review the documentation to get the full story.
3) Again they say lmreread works but based on experience my team still does the stop/restart to ensure the clean import of the option file changes with no delay.
4) Most software vendors give a grace period to reacquire the license which is any where from a few minutes to a few hours and in some cases a few days. Again it depends on the vendor.
5) I have never heard of an alternative and I have been doing license management for almost 20 years.
Here is the link to our statement regarding license servers on VMs:
Regarding the options file, it often depends on what you're changing but you need to remember that you can make changes for licenses that are currently checked out. If those changes conflict with the state of the current checkout, the results of a reread can be unpredictable.
Also, given the wide variety of applications within Mentor and their respective consumption models, we can't guaranty that a restart won't cause a problem for a running application. However, in general, interactive applications will retry and some will throw a dialog to alert the user. Batch applications like simulators will usually finish their current operation and wait to reacquire a license before moving on. There are some applications that may never reacquire their license if the restart takes too long.