It's just some shitty catch-all /v/ meme. It doesn't have much in the way of an actual meaning apart from the usual "thing I like good, thing I dislike bad". Even putting that aside, it seems fairly ridiculous to say that a terrible VN adaptation (of a game that was actually a passion project and has "soul" going by your definition) of all things has "soul".
most anime are adaptations of passion projects, as has been discussed before in >>75134
, and what people see as passion is probably the majority of the time derived from the source material
"Soul" and "soulless" are the same as "passion" and "laziness"; they're words used to talk around a work rather than about it. Saying something is good because it has "soul" is the same as saying it's good because it's good.