Yes, there's going to be a fleshed out story mode - when you select story mode, it will soon give you that introductory scene, introducing the MC, the setting, and the tone of the story. There will be character creation, still, with the ability to customize some aspects of your looks, some background info that ties into your starting resources, name, etc. Even in story mode, the game will play in that roguelite fashion, but with some dedicated, automatic encounters added that move the story along and ultimately end with some story conclusion - not necessarily the same one every time. To answer that point - most of these set encounters will take place in dungeons and towns/cities.
Strategically moving from encounter to encounter on the world map is going to be a large part of it - although you'll also have movement within large cities and dungeon-areas. On the other side of it, customizing your character with skills / stances / spells / perks and gained knowledge will be a big chunk of the "RPG" part - right after the actual role playing of selecting how your character responds to situations when they have a choice.
As for the core "femboyness" of the game - what's currently in is not totally representative - it's very skewed toward combat encounters, with no way to avoid them, and very few meaningful interactions in the way of flirting, or being cute, choosing to explore more feminine attire/mannerisms/fun times, or encountering the same character multiple times and building a relationship with them, or just the character inside their own head thinking about the situations they find themselves in and how to respond to them. There also aren't currently the various attributes and customizable options that will allow your character to become more femboy-like, or more sexy, or to (potentially) keep chaste and merely have femboy-like qualities.
tl;dr - it's not going to be all click combat click - that's definitely over-represented in the current build. There are a lot more RPG elements and femboy-y elements coming down the pike - it won't all be monster girls with dongs going into the MC's face and butthole.