Yes, it'll boost your total points.

Example:

Regular Playing Hours

Assuming you bought in for $8 (8x) which is equivalent to 8 points, then you hit a Straight Flush Flip Bonus which gives you 4x your buy-in in extra points:

$8 (buy-in) x 4 (Straight Flush Flip Bonus) = 32 points + 8 points (your buy-in) = 40 in total points

Happy Hour Boost

If the above scenario happens during Happy Hour, you will receive 1.5x of your total accumulated points which includes your Flip Bonus (if any)

40 points x 1.5 (Happy Hour boost) = 60 in total points