Thanks for your report.

What locale is your system set to? With 52.0.2705.0 on 10.11.4 in en-US the following steps work as I expect:

1) Focus the omnibox
2) Type Option-R to make a "(r)" symbol
3) Focus a text field in a webpage
4) Type Option-R to make a "(r)" symbol

Option-E does not produce any character for me.

I'm on 51.0.2705.0 Canary on 10.11.4, same setup as you.
Chrome is configured to just English. My OS is also configured to English.
This is normal functionality supported by MacOS (even when you're configured to English, you can still type accented characters). The ® symbol works, but accented characters don't.

To see how it works:
1) Open TextEdit
2) Type Option+N, then the letter a.
3) You should see the following character: 'ã'

To reproduce:
1) Go back to Chrome Canary.
2) Follow steps 2 and 3 above.
3) It will only show the 'a' character, not 'ã'.

To see how I think this is a regression:
1) Go to Chrome Stable (49.0.2623.112 for me).
2) Follow steps 2 and 3 above.
3) It will properly show the 'ã' character.

Other characters you may want to try:
- Option+E, then A -> á
- Option+U, then U -> ü
- Option+I, then O -> ô

This is actually pretty serious, it could make the browser unusable for work or study for people in many regions :/