Wolfe wasn't fired until halfway through season 2, and all but a few of season 2's episodes were scripted or at least plotted under his tenure. So it wasn't until the latter part of season 2 that the show diverged from Wolfe's plan.
As for not knowing about Engels... Trust me, you're far better off.
What I liked about Andromeda is how the cast worked on shedding the various bits of alien makeup. Trance, Tyr, Rev Bem... systematic changes for become human/having less time in the make-up chair.
As I recall, Trance's makeup change was imposed by the executives, rather than a choice by the cast or writing staff. The loss of her tail was due to the failure of the makeup/FX department to come up with a way to make it look good and move convincingly. Not only was the show made on a shoestring budget, but its makeup team had very little experience with prosthetics and creature effects and just didn't have the skill to do it well, so their attempts at nonhumanoid aliens were pretty dire. As for Rev Bem, Brent Stait left the show because he had an allergic reaction to the prothetics and the glue, and so he had to leave. The later simplification of his makeup was done to make it more feasible for him to return on occasion.
As for Tyr losing his arm spikes, that was just weird. It was probably another budget-saving move, like everything else about that cheap-as-hell show.
