From what I understand the spells would be treated as lower level, but at the moment I don't have a source for you on that. Perhaps someone else can provide it.
As for why Silence is under Time... I didn't write the class so I have no comment.
as the patron spells are becoming part of your spell list. that mean they are treeted like any other spell on your spell list. including the fact you use their said spell listed level as their level for casting them or using them on items.(unlike say, wizards who all have the same spell list. each witch has a slightly difrent list depanding on her patron and in each there are spells that might be on difrent level then normal wizards spells. but for that said witch that is the level she uses for that spell)
silence is there for the special effects when you haste or slow some1 ;)
Being that the patron spells can give you spells that aren't even on the witch list, it is reasonable to assume you use them at a level appropriate to when they are gained.
This does create some oddities though. Technically you have the spell on your list twice. Meaning you can prepare both level 3 and 4 ice storm. But the weirdest is what happnens when an option delays your rate of gaining these spells. For instance, a winter patron with the familiar patron option wouldn't get ice storm till 7th. So in that case would ice storm be a level 4 only spell?
im pretty sure that any spell on the patron list is not on the normal witch spell list.this is not like a sourcerer who gain axtra known spells so the bloodline give extra spells that he might have taken allready.as the witch can teach her familier new spells(by feeding him the scroll,read about it).but i might be wrong.
i am not familier with the option you mantioed taht delay the spel lprogerssion. isn' any witch's familier also a patron familier? (given form the patron etc?)
If you gain the spell at that level, you can cast it as a spell of the level you have just gained for WItch.
Think of it as this. Like Oracle and Sorceror, a witch gains a bonus spell
known per spell level castable to her, except level 0.
So, the spells, in order are: Lvl 1, lvl 2, lvl 3, lvl 4, lvl 5, lvl 6, lvl 7,
lvl 8, lvl 9.
If a spell falls into a particular segment, it is a spell of that segment's lvl for you.