The TE-40 is a good guitar or the SC custom or the 550s are definitely better?
It is a false belief that guitars can be evaluated on a simple value range. This question cannot be answered. Some will tell you that the SC-550 is clearly the better choice because it has a finely detailed flame top (which is true) or looks oh so much like the Les Paul they've been adulating since their teenage years. Others will tell you that the Les Paul shape is a clumsy thing with bad balance and failed ergonomics. The same goes for tone. There is no value scale there either, you might as well ask which of chocolate or vanilla ice cream is better.
These three guitars are all fit to purpose. They just have different characteristics. Their objective qualities as a music instrument, which include ability to be set-up properly, hold tune and have functioning electronics, should be roughly equivalent. The more expensive ones might have nicer finishes, big perloid inlays instead of dots on the fingerboard or even smoother, higher precision tuners (on the SC-Custom).
The
decision between TE or SC is an important one, though. These shapes and sizes are different enough to form habits and those who learn on one are not always happy with the other. The TE-40 clearly has the better ergonomics and will be more pleasant to play sitting, which beginners do a lot. Should one favour the shorter Gibson scale and size, the SG, copied by the Harley Benton DC models, is the answer to the ergonomics and weight matter.
Regarding the
choice of bundle, the 40W amp with a 10" speaker will be louder than you need for home use, unless your home is in the woods and you live there alone. My 20W Fender Mustang is also louder than I need and I use it with the master volume on 2 out of 10. The larger speaker and enclosure of the 40W amp will very likely have a positive effect on tone but I wonder if this will happen at reasonable, home playing volumes. Hopefully someone with that sort of experience can comment on this.
A critical point with such amplifiers is how they distort and at which level they do it. This is why I would rather advise a beginner to start with a modelling amplifier that can do all possible things at low levels. You don't need any of it to learn the basics but I'm sure a beginner wants to be able to fool around with the palette of guitar sounds. The alternative to this is to add a multi-effect device, preferably bought used (I got a VOX Stomplab for 25€ on ebay, it's great). This way, the bundled amplifier can be used clean at any level is appropriate and be fed anything from acoustic simulation to high gain metal and worse (yes, there is worse). Just be aware that the common Harley Benton HB-20 or HB-40 won't provide all possible guitar sounds unless it gets help.
The three guitars listed above have
humbuckers. If you know what you're doing, fine. If not, check the difference with single coils, just to make sure you don't buy vanilla if you prefer chocolate. Yes, it's that sort of difference. If you find you like both and cannot choose, get a guitar with both or with a coil split function (the SC-Custom has it, not the other two).
Some people like to play through
headphones. They don't need a big box with a speaker. They can plug into a computer and use free amplifier emulating software. Or just use some multi-effect unit as a replacement for the amp. And if they do want to make noise, that computer or effect unit can be plugged into their stereo or whatever TV or home theater thing they have.
I see some talk about
guitars and styles. Most guitars can play almost anything. Jimmy Page recorded the first Led Zeppelin album on a Telecaster.
If you need to look like you belong in a scene, you need a guitar that looks the part, whatever that is, but unless one aims at replicating sounds exactly, the choice of instrument does not matter much at home. Get something you like to look at and that doesn't stand in the way of the sounds you want. As an example of the latter, if you like clarity and hearing the attack on the string as you get from an acoustic, do not go for vintage humbuckers, they'll swallow it.