If the 650 you've had fitted has been fitted with a Glass Tamper Sensor, a Dual Zone Proximity Sensor and a Tilt and Motion Sensor, then that brings it up to the same specification as the 950 to the end user.
The 950 has onboard relays which make life easier for the installer, but that's about it.
To be honest, whoever has fitted this alarm for you have done nothing wrong and although they have technically fitted the wrong alarm, they've brought it up to the same specification as the one you were originally quoted for.
Yes, I can and would do it cheaper, but only because I've done so many Supra's I know them inside out. I know where to mount the units, where to tap into the correct wires without even needing to test most of them.
People like GAP do them cheaper because they don't do a proper job. They'll not immobilise the car properly, or leave out sensors, leave parts of the system not set up, make 'twist 'n' tape' connections, and generally bad fitment, that's their reason for doing them cheaper.
What they have charged you isn't unreasonable. It's less than the RRP price. In your opening post you knew it was a 650 and seemed happy with it. As long as they have fitted it properly and it is working as it should, I really can't see the problem.
Keep on their good side. You may need their help if something ever goes wrong. - And I'm not saying the alarm or their work, but imagine one day, you car doesn't start. The first thing people blame is the alarm. If this happens to you, and you get them to come out to look at the alarm and they find a fault that's not alarm related, you'll wish you were on good terms then!