"Because I submitted an extension that gives me until October 15th to file, can I avoid being penalized on my roth 401k excess contributions if I take out the excess by that date?"
No. The tax code specifies that deadline to receive the corrective distribution of an excess 401(k) employee contribution is April 15 of the following year, not the due date of your tax return for that year. See IRS IRB 2007-22: https://www.irs.gov/pub/irs-irbs/irb07-22.pdf
