My wonderful LBS gave me store credit when I swapped out the standard parts right away and upgraded (along with a small store discount for accessories/upgrades the day I bought my bike). So, if you do get store credit by swapping immediately and upgrading, that's what I would do. I'm a new mountain biker, but my LBS said that they highly recommend the tubeless tires for mountain biking due to less weight and less worries about needing to change tubes/tires from thorns/sharp objects.

If you don't get store credit by immediately upgrading, then just wait until you are sure about what you want.
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2012 Specialized Amira Elite, upgraded carbon handle bars, Jett saddle 143mm switched to 145mm 2012 Selle Italia Max SLR Gel Flow saddle

2011 Specialized Ariel Sport,suspension post,Serfas Rx Women's Microfiber saddle