If you're simply reloading - meaning effectively recreating what could easily be a factory load, not particularly suited for any given rifle - then you're not fully realizing the potential of your rifles, but you do garner the "advantage" of being able to prepare generic ammunition which works well enough in any of your firearms of that cartridge.

The small base resize won't well fit your bolt gun chamber, then I would hope the headspace matching well to try to center on the shoulder, else that cartridge will be swimming around in the chamber. What's the base-to-ogive length for your selected bullet in each rifle? The headspace length?

How precise of ammunition are you wanting to produce? If you're just reloading, not really handloading, then you'll likely be able to find a load which works fine in both. If you're wanting to handload and find an optimal round for either rifle, then small base sizing for the bolt gun won't bring any benefit.

However, as long as you're getting a well fit headspace, in 30-06, you likely will only see a very slight shift in precision, if you see any measureable effect at all.