The three inspirations for the game from the very beginning were Minecraft, Fallout, and The Walking Dead.
From Minecraft we get crafting, unit block building, exploration
From Fallout we get post-apocalyptic RPG elements like the traders, quests, and player progression
From Walking Dead we get zombies, setting up and defending a base, and survival
All of this was in the minds of the creators when they made their plans, did their preliminary prototype for kickstarter and then continued into early access on Steam. They NEVER said, lets build a survival game and then as they continued on added crafting, and building, and RPG elements as appendages to the main idea of survival. They NEVER said, lets make a tower defense game and then tried to mesh in elements of survival and roleplaying as supporting gameplay options. The idea itself was that it would be a hybrid game and they have pursued their goal without deviation from day one.
Sure, they experimented with HOW those goals might be implemented and some people became enamored with some of those experiments to the point that they thought that those implementations were the point of the game. For example, Learn By Doing was a method to push player progression and after experimenting with it they chose a more traditional (and much more Fallout-esque) method of central experience pool for purchasing advancements in progression. So their goal of player progression as one of the elements of the RPG genre that they wanted for the game never wavered but the way they implemented it changed-- for better or worse depending on who you talk to
Before Alpha 11 there was no RPG elements to speak of other than progressing from primitive tools and weapons to better tools and weapons. Those weapons and tools didn't even have tiers of quality. So for 10 alphas there were no RPG elements to the game to speak of because they had not reached the point at which they felt it was time. In Alpha 11 we got the first push which was that every time we crafted a tool we could craft a better one with a +/- 50 randomizer. For the first time ever in the history of the game "spam crafting" became a thing and it was a huge game changer and the only form of progression in the game. From Alpha 11 until Alpha 16 various forms of progression and experience cocktails were experimented with as well as the role of books and schematics and what advancements could be purchased with points and which would be learned by repeated action. Finally, in A17 the final decision about how players would progress was made and it has been built upon until now.
My point in relating this history is that to the casual observer it might appear that RPG elements were not originally conceived to be part of the game but were tacked on later. But this is far from the truth. That this game would be a mix of survival, tower defense, and RPG was planned from the beginning. If past studios have always started with one pure genre and branched out from there then I can definitively state that the approach TFP took was ground breaking because they did not start out at all focused on a single primary genre. But I suspect, that this idea that a studio must start with one primary and all others are secondary to it is a misconception and not true at all. I doubt TFP were the first, although they have been quite successful.