I'm not sure what you're asking exactly. If it's worth it to upgrade the Encore? I would lean towards no since you'll probably end up in a position where you've put more into parts than you paid for the instrument and still have a low quality instrument due to the neck and body construction.

Can you upgrade it? Probably, However, not all exactly the same are so depending on what you're doing be sure to make sure measurements match up.

Unless you really like this guitar, I don't think it'd be worth upgrading, but it's personal preference at the end of the day. If this guitar is just totally you, then do what you think is best. If you hate how it feels to play and it's been given a proper setup (intonation, neck relief, string height) then you're probably not going to get a satisfactory result without putting more than the guitar is worth into it.
There are two basics:

What do you want to upgrade? It is a good idea to have a clear idea of what is wrong with it as-is, before you start upgrading, because "more" doesn't necessarily mean "better". My favourite electric cost Oz$65 from the local hock shop, and the only thing I had to do was a set up. The pickups, for example, were fine, and I'm demanding of pickup performance. The attractiveness of upgrading also depends on how much is DIY. For example, I don't mind doing fretwork, but I wouldn't want to have to pay someone else to do it for me on an inexpensive guitar. Even then, the cost of suitable tools has to be taken into account, and might not be worth it for a one-off job.

You won't recover the upgrade cost on resale, it is essentially a labour of love. What you get from customising a cheap guitar is mojo, but it isn't transferable.
I'll have to agree with tony. with a cheap guitar, you're not going to get back what you put into it if you decide to sell it, so you'[re doing it just for a guitar you intend to keep and play, and like.

Same as he said, I picked up a Fender Squier and all I did to it was a setup. I eventually had to replace all the pots, cheap junk and started going bad so I replaced all 3. That's all I ever did except replace the pick guard, it's the one in my avatar. Got it for sale at a local shop, quick install and it looks a lot better than the plain white one it had. never touched anything else, the pickups were great, still are.

As Tony said, get a feel for the guitar and figure out what you want to improve before you start throwing money and parts at it. if you want to replace pickups, check around at music stores that work on guitars first, often they will have good used pickups for a fairly good price that are just fine, someone just wanted to throw a lot of money at the latest whiz bang pickups. I got 3 or 4 at a shop in Louisiana for $5 each, one was Peavey single coil like those used in their T60 guitars, fantastic sounding thing, I loved it. Sure did hate to have to sell that guitar...also got a couple of single coils, one went into an old el cheapo and made it sound twice as good. Still have a pair of chrome humbuckers I've been trying to decide what to do with for years...$5 each...still thinking about building one...

I don't worry about tuners, if they hold tuning, they're good to go. A drop of 3 in 1 oil once or twice a year will keep cheap tuners in good shape for 20 years. Been there done that. I'm using a 1966 Harmony with open back tuners that are over 30 years old right now, still working perfect. the cheap tuners that came on the Squier are still working fine, I've played it onstage for over 20 years, and it's my favorite guitar. if you look around you might find a cool looking pick guard, that can make it look better, but most of the factory parts are usually sufficient if they are working right. The main problem I've found with cheaper guitars, like my Squier, is the pots. Those are often cheap chinese garbage, get good ones to replace them with.Anything else, just depends on if it needs to be upgraded or not.
Hmmm...I wonder what this button does...