frida,
assuming you have the data ready - otherwise prepare in surfer or similar progs you prefer -
feflow 3D layer configurator: maybe you could start building your domain with the lowest slice - the bedrock, fix all slice elevations, extend your model upwards with the slices needed, keeping 0.1 meter distance between the upper existing slice, import the elevations for each slice above bedrock, fix each slice before importing the next above, always allowing feflow to set the minimum distance of I would say at least 0.1 m, adjust kf where these thin layers should not exist.
as you have mentioned mountain peaks - keep an eye on the interconnection between the bedrock an the sediments above (confined? specific BC?)
salve