Just my opinion..... you have to make the decision on what's important to you! IF the sights are important to you line them up. If you can chamber factory then I'd stop with that, good enough. If you can't chamber factory rounds and you ever think there'll be a need then either rent a reamer for about $30 and take the 4 or 5 thou out or take it to a gunsmith that already has the reamer and let him correct it.
If you don't think you'll ever need to shoot factory ammo then just line the sights and continue to size to the chamber, there's certainly no harm in doing so. Should the rifle ever go to someone else though I think I'd pass the chamber irregularity along.
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