As you've probably found out DOT 5 and DOT 5.1 are very different products and will not mix. If you decide to use 5.1 the whole system will need flushing. I was advised to carefully consider it's impact on standard seals as it may be adverse in the longer term.
Yes DOT 5 is a silicon based fluid and will not mix with any other fluid, however as far as I understand 5.1 is a glycol based fluid and is compatible with Dot3/4. The advantage being higher boiling points. I have not found any comments on damage to seals on 5.1 . However as I do not take to the track I really do not need the extreme higher temp. Although I do like the ATE Dot4 fluid as it does have a higher dry/wet boiling point to the OEM fluid and comes in two different colours so you can tell when the new fluid has reached the caliper being bled.