I would not worry one bit about the boot. It's made of the most durable silicone. I have sold over 200 of these shift kits, and with well over 600,000 miles on them, not one has been reported to be showing any degree of wear. In fact mine has almost 11,000 miles on it, I greased it once and never since. The tolerances in the area of 2nd gear are very close, no worries here either. The transmission is already seated in 2nd before any, if any contact is ever made.
I'm willing to bet you love the shifting correct? Enjoy it, It's all good.
If I can help in any way just let me know.
Thanks,
Jamie
Mazda Performance Parts & Accessories // JamesBaroneRacing.com