TinyMCE 4.x was a significant re-write vs TinyMCE 3.x and required significant changes in our integration.
The legacy settings were removed because they only apply if using the older version. However we made it possible by configuration to go back to the old implementation in case any major problems came up with the new one. ie one could change TinyMCE:UseV4 to false and then restore the old values and settings. But we hope no-one needs to do that and we try to remove un-needed settings from web.config when we can.
I always recommend use the new Web.config to make sure you have the newest settings and because it helps to eliminate legacy settings that just add confusion. So it is better to restore customizations to the new file rather than port changes back to the old file.
Generally the only things you need to maintain in Web.config are machinekey and settings related to enabling larger file uploads. database connection string and smtp settings should be in user.config which is never touched during upgrades.
Hope that helps,