I didn't notice any significant downsides to using the padded slings with my vests which is why all mine are padded, so they're comfortable with or without a vest.
To answer your question, yes, the shoulder pads/straps of most vests are generally stiff enough that they spread the load over a wider area so the padding on a sling doesn't make much difference comfort-wise.
As I didn't find the sling padding a hindrance when used with a vest, I opt for padded as it's more comfortable when I do sling a long gun without a vest.
Max
P.S. figured I should mention, another factor in how much you'll need to shorten the sling is where your 2 mounting points are located and how far apart they are.
The 5 padded VCAS slings I have go on different long guns from AR's to SCARs a Tavor and a Benelli M4.
With the closest mounting points, I am close to maxing out the adjustment buckles to get a snug shortened length when worn without a vest, but it's fine.
If you get the version with the Cobra quick release buckle, that section adds length. It's an added factor (and cost) that's unnecessary if you use any kind of QD attachments (whether it's push-button or HK) as opposed to setting it up hard-slung (no QD ability).
Hard-slung (sling looped through slots/attachment points) can use up some length so adjusting it short enough will be less of a problem. Long enough hasn't been an issue for guys with 50"+ chests, unless they're ginormous gorillas.