Hi Itzafugasi,
Yes, we recommend customers add company.com as an alternate UPN suffix. The alternate UPN suffix will not implicate your current AD users. If users in your organization do not have route-able UPN suffix email addresss (such as user@company.local), they will be synced to office 365 and given email address user@company.onmicrosoft.com. However, if the user logon name is user@company.com, it will be synced and keep the email address user@company.com.
Yes, once you have added your domain company.com in Office 365 and deployed the AD FS 2.0 and SSO with this domain, users can use company.com as UPN suffix to log on to Lync Online.
The changing UPN suffix will not affect the way the user authenticates; it is configured for particular user. For example, if user1 has logged on name user1@company.local and user2 has logged on name user2@company.com, user1 need to type user1@company.local to log on to the domain-joined computer, and use user1@company.onmicrosoft.com to access Office 365. However the user2 can use the account user2@company.com to log on to both computer and Office 365. That is why we recommend customers to add company.com as an alternate UPN suffix to realize the Single Sign-On.
Thanks,
Bourne Zhang