This is sort of a general concern with a sect-based flavor added in.

I noticed that in order to be able to use my sect spell prep, I will need to know alternate preparation and silent preparation. I'm not sure if this differs from sect to sect as some of the sect preps arn't "silent."

I don't see why the obtainment of a sect preparation should require the use of two spell slots. A spell prep is hardly anything of great game balancing impact and is mainly cosmetic. Yes, I understand that one of these feats makes it possible to use spell preps that make it easier to hide your preparations and so may warrant a spell slot. However, why should simply being able to use a different spell preparation also rise to the cost of a spell slot? I think that this first feat, alternate preparation, should be free. It does less than FM or even cantrips which all cost no slots.

Illusory preparation is likewise similarly just a cosmetic feature and shouldn't cost a spell slot in my opinion. We already paid/will pay a price for those preparations when they were/are obtained. Having them not cost a spell slot, breaks no great balancing regime as there is nothing really gained except for some cosmetic changes which don't add up to a spell slot cost.

Perhaps you can give alternate and illusory preparations some mechanical advantage above regular preparations that would have it make sense for their use to cost a spell slot?

Also, I think the sect spell preparations should be limited to the basics of needing alternate preparation. None of them seem illusory and only Heritage House and the Monks seem to have ones that might fall under the silent preparation category.