I can absolutely relate to your confusion, especially since I started working with Check Point at the R80+ level.
"IPS" layer => is used to manage IPS on sub R80 gateways (at least one sub R80 gateway with the IPS blade enabled must exist on the related SMS in order to have this layer)
"Threat Prevention" layer => is used to manage the IPS on R80+ gateways
The difference lays in the detail; so for example the "protected scope" (or source/destination) settings that you mentioned are configured differently - depending on the actual layer, either IPS or Threat Prevention.
The newer Threat Prevention layer for R80+ gateways offers the possibility to set a protected scope for each rule/profile where only specific hosts or networks (etc...) can be mentioned. As you see this can end up in a quite granular filtering process when it comes to use a specific profile only for a very limited amount of devices in your network.
On the other hand, the older solution, configured via the "IPS" layer also offers columns as "source", "destination" or "proctecion/site/file/blade". The difference is that you are unable to configure anything in this place. If you want to achieve some sort of granularity you need to open the specific gateways for which the IPS traffic applied and select "IPS" => "Protection Scope". Here you can choose between "Protect internal hosts only" (hosts behind an interface declared as internal) or "perform IPS inspection on all traffic". That's everything which is possible. In addition to that you have more options with the "Threat Prevention" layer in general, also when it comes to the exceptions in place.
Also; if you are asking yourself what the difference is between "protected scope" and "source" or "destination"... its quite simple. While source or destination lets you specifiy whether a rule applies only from a specific host/network to a specific host/network the column protected scope does not care about the direction, and therefore applies this rule if the mentioned host is either the source or the destination of a specific connection.
PS: In general, the "Threat Prevention" layer for R80+ gateways offers much more flexibility when it comes to Threat Prevention configuration. This can also be seen in the track column, where pcap creation is possible - this does not work for R77 (IPS layer) gateways - at least not in the same place and with the same granularity. The same thing is present for exceptions.
If you are interested in the details I can recommend the "IPS Immersion Training" by @Timothy_Hall - you can buy the video course and documenatition on his web site. It definitely brings some light in the R80+ IPS configuration, and also gives you insights to the past.