When you say you can't remove the traits, are you saying that unchecking the "trait is active" box does not work? If so, is that only for specific traits, or all your traits?
Yep, what the OP describes is definitely not intended. We've confirmed it internally and bugged it. OP: thank you for the heads up, and all the details in your post. Very helpful.
We've confirmed this issue internally (the "no Venture costume" issue). Due to the nature of the bundle, the Venture comes packed in a box, which is not the case if you just buy the ship individually. The error happens only if you get the Venture from the box. So ... Try this workaround: discharge your Venture, then…
Try slotting any reputation project. You don't have to complete it, just slot it. After that, the sponsorship projects should show up as an available upgrade.