I believe the +1 or +2 bonus is not based on how easy the item (potentially) is to reach, but instead how obviously the item and the power go together.
For example, if I have a glowing sword that can cut through anything, it's seems pretty obvious that the glowing sword and the ability to cut through anything probably go together. So if you took my sword away, most people would expect me to also loose the cut through anything power.
However, 'just a necklace' doesn't seem to be directly related to being a better shapeshifter. If you think it should have the +2 bonus, you should think of a way to make the fact that it grants you power more obvious.
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As for modular powers, if he already paid the -2 refresh surcharge once for modular powers, then there's no need to make him pay again for the item of power to enlarge his modular power pool.
So, for example, if his character sheet could look like:
Echoes of the beast -1
5 points of modular abilities -7
item of power
(somehow obvious necklace) +2
3 more points of modular abilities -3
total cost -9
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If you have modular abilities power, any of the (strength, speed, toughness (which includes recovery powers)) powers are supposed to be available to you, plus whatever creature features or other powers the GM will let you get away with.
Probably, your catch for any toughness powers you get via modular abilities should be fixed when you buy modular abilities, so you can't just shape shift to something with a different catch.