you should be OK as long as you set the sequence frequency to the minimum note rate (i.e. the rate that steps index) or higher. If it is lower by half, for example, you will reverse the effect on each pass through the sequence. Triplets at a lower rate will perhaps be interesting, but messy, and so on...
The only thing you might do is try to figure out a way to trigger the LFO to "restart" simultaneously with the sequence start...might be a patchable way if you think about it.
You could also use the AD envelope which has an easy path for patching a trigger