The second form feels more natural.

Il risque de vous encombrer plus que de vous être utile.

Il risque plus de vous encombrer que de vous être utile.

Imo if there is a slight difference it may be on the accentuated verb. In the first case "he" would be "bothering" and a little bit "useful", though you might have said:

Il risque de plus vous encombrer que de vous être utile.

In the second he "risks" to just be a pain.

I don’t think there is a difference in the meaning of both sentences.
The only difference is style, because “plus” is in the middle of the sentence (we use proposition for this case in French, I don’t know if the literal translation “proposal” fits), and so it breaks the flow a little and the sentence seems a bit clumsy.
As a French myself, I see the first version far more used both in text and in speech. Second version is correct nonetheless.