missing 1/4" outputs is not a big deal - there are plenty of 1/4"->1/8" cables - I generally use these...
as for headphones - only really needed if you intend to use them away from what you regularly plug into - a mixer or an audio interface, as these usually have headphone outputs - alm make a very small headphone module - alm hpo
or get an end of chain mixer with a headphone output included
as for case - buy the mantis, buy as few modules as you think you can... ie a minimum viable synthesizer (sound source, modulation source, sound modifier, a way to play, a way to listen) and a few utilities - a quad cascading vca is a good investment & can be used as a mono output... and get some blind panels (or make them out of cereal boxes) to cover the holes!!! buying a case that you know you will run out of space in is a false economy!!!!
"some of the best base-level info to remember can be found in Jim's sigfile" @Lugia
Utility modules are the dull polish that makes the shiny modules actually shine!!!
sound sources < sound modifiers < modulation sources < utilities