You did [miss something].
James's answer above [this post] is a good reply but [it is also] terse. Tᴚoɯ's reply is fuller [than James's reply] but slightly misuses its terms.
If something seems too good to be true, it probably is.
The expansion of the main clause [of this conditional sentence] repeats the entire subject complement of the 'if' clause that comes before [it].
If something seems too good to be true, it probably is [too good to be true].
'To be true' is just an object complement describing the way in which the thing is 'too good'.
To step outside the somewhat tautological grammar terms, though, it may be helpful for you to realize that [the sense of the word] 'seems' [being used here] means
- 'appears to be'
- 'to apparently be'
- 'to be ~ in appearance'
Your conditional [sentence] could be rewritten
If something is too good to be true in appearance, it probably is too good to be true in reality.
because the 'is' in the 'if' clause is being contrasted with the 'seems'. That [situation] gives it more weight than [is] usual. It's an emphatic sense of 'be' that means 'to truly be', 'to really be', 'to be ~ in reality'.
Of course, written this way, you couldn't leave out the end of the main clause. If you wrote
If something is apparently too good to be true, it probably is.
people would probably understand [what] you [meant] but grammatically—like [it was] above—the main clause should be repeating the entire subject complement.
If something is apparently too good to be true, it probably is [apparently too good to be true].
including the 'apparently'.
You could sidestep that by including an adverb
If something is apparently too good to be true, it probably really is [too good to be true].
but that's much wordier, which is why the proverb is expressed the way [that] it is.
Edit: I think you understood that point about 'be', which caused your confusion. The mistake is that when you changed the sentence to read, 'if something seems to be good to be true, it probably is true' you also changed the antecedent of the second 'it'.
If something seems too good to be true, that something probably is too good to be true.
If something seems too good to be true, it probably is true that that something is too good to be true.