The problems with tangs that are not fully seated while it is at rest is that they are "springy". For instance, if they're a little bit proud to the wood, the bolt certainly can be tightened down to bring it flush. but there will still be something of a gap under it that can create repeated flexing and unflexing of the tang during the setback of firing. Heavy loads will flex it more than light loads, but the seasonal movement of the wood will create varying amounts of load on this new "spring", and could vary your point of aim slightly from day to day.
The best thing to do is to get your tang bent (most can be bent cold, but heat will make it easier and soften the steel) to a position that's pretty close to flush (but slightly proud) while it is at rest, and then do your bedding (whether in wood or with synthetic substances) I like synthetics because it's easy, and 100% effective in giving full contact. Clamp your barrel down at the breech, and bring both surfaces to flush with one another. You could use a flat-head bolt through the tang hole to help hold it down too, but the general idea is to bed it while it's in a relaxed state. If you do that, make sure to deepen the screw slot so you can get it back out after it's been filed. Just don't use the one you intend to be your finished gun tang bolt, because it's going to get buggered up during the filing. You may need to freshen up your counter-sink after the filing for the tang bolt, but that's pretty easy. Now you'll have a tang seated that is rock solid and will never move on you.
Don't worry about getting the tang filed too thin. As they come, they're about 1/4" thick, which is way more than you need. You only need about 1/8" (and maybe not even that much) for strength if everything is bedded correctly.
One more thing, is to make sure you have something of a small gap at the rear of your tang for it to set back and then reset a little during firing. Just an Exact-o knife's blade width is enough. If you don't leave that little gap, the tang will slam in to the rear of the inlet and introduce cracking of the wrist over time. That is particularly a concern with tangs that are rounded or shaped. They become something of a wedge.