I can speak to the first part of your post as a former IRS employee and now EA that currently negotiates IRS settlements, etc., as you go forward into the future.
You have a filing requirement to file your personal tax return by April 15th every year (holidays, etc., make it the next business day) if you meet income/filing status requirements as indicated in IRS Publication 17, Table 1-1, independent of whether you are due a refund or not.
You are not penalized for filing your return late if you have a refund, but you’re considered a late filer which is noted in your account with the IRS (which is what could cause a potential Guideline F issue based on my understanding). Technically the IRS could file a penalty even with a refund, but I’ve never seen that.
If you file an extension for your return on or before April 15th and you are due a refund, you are considered in compliance if you file your return by the extension due date (October 15th). The three-rule is to claim a credit or refund, the tax return itself is due April 15th of the given year.
If you file an extension for your return on or before April 15th and you owe tax, your tax is due in full on or before April 15th.
There is no extension to pay. The extension is for the tax return only.
Most common reasons you are subject to a penalty. In general if:
a) you file your return late with no extension and have a tax bill;
b) you file your return on time but didn’t pay enough tax throughout the year (through withholding and/or estimated tax payments) resulting in a balance due greater than $1000 even though you pay your balance in full with your tax return;
c) you file an extension for your return on or before April 15th with a known balance due of greater than $1000, pay the balance of greater than $1000 in full as an extension payment, but file the tax return after the extension date; or
d) you file your return on time or by extension and the amount of tax you paid in all year via withholding or estimated tax payments is less than 100% of last year’s tax due (110% if high income earner) or less than 90% of this year’s tax due.
All tax for the year is due in full by January 15th either through withholding tax or as estimated tax payments.
Estimated tax payments are due April 15th, June 15th, September 15th and January 15th of the following year.