Typically you have to pay a little bit more for a prebuilt PC but It really depends on the prices the builder is charging. With some holiday sales, you might pay $100 or $200 more than what it would cost to build the system yourself. You might break even with a really good sale. The only constant I've seen with sub $1000 prebuilt systems is they use cheaper motherboards, cheaper power supplies, and cheaper RAM.
The warranty on a prebuilt system is a catch 22. The parts that are used on a prebuilt PC are considered to be OEM parts, so many manufacturers, but not all manufacturers, will not honor the warranty because the company that built the PC is responsible for the warranty service. Most prebuilt PC's come with a 1 year warranty whereas the retail part will come with a 3 year warranty. When troubleshooting a custom built system, in many cases the motherboard manufacturer will help you figure out which part is bad..... mostly because the motherboard is often the source of the hardware failure and they want to make sure the motherboard is not the source of the failure.
Asus is one company that does not require an retail invoice, so you would be able to RMA the motherboard after the builder's warranty period expired. You would just have to find a socket cover if the part is an Intel motherboard. MSI has also been know to not require an invoiced, and MSI has been known to be flexible in some cases. Gigabyte will not honor the warranty on an OEM part. EVGA is also questionable but they've been known to bend the rules sometimes.
You can normally upgrade a prebuilt system but sometimes you will not have as many upgrade options as you would if you had built the system yourself. Intel h310 and AMD a320 motherboards are commonly used in prebuilt systems, but these boards suffer from low chipset based PCI-E lanes which limit storage drive options. h310 and a320 motherboards come with 2x RAM slots which limits the maximum amount of RAM that can be installed. a320 motherboards in particular are limited with CPU upgrade choices. The other problem with prebuilt system is they use the minimum power supply, and sometimes thee companies will use a power supply that's smaller than what's recommend for the Graphics card. You can always upgrade the power supply in the future when you want to upgrade the Graphics card, but this will add to the cost of the upgrade.