Hello, I was just wondering. For clix with effects like +5 start with equipment. or to gain some effect. Is that treated as there total cost for other effects at that point?

Example. The new Apocalypse, is 295 and has +5 to start with a sword.

If a clix has an effect that checks to see if a clix is weaker or stronger in cost than them. And they are 300 points. Is Apocalypse weaker than them?

Optional traits do not raise the point value of a character. The point value is and raises the number(s) printed on the base of the figure.(Comprehensive rulebook: 1.1 page. 1)

Apocalypse is "Weaker" than a 300m point character in the example because his point value is 295.

Thank you, Been wondering that for awhile now, but it never came up in our games, till all these new pieces with swords.

Relevant rule with important part bolded:

Doing a quick search for Point Value in the CRB I missed that.
Good work.