Wvishere,
WELCOME TO THE AWS WELDING FORUM!!
A couple of points to add to the information John posted...
1) The engineer can call out larger weld if he so desires. No clause 'overrules' the engineer. See Clause 1.4.1.
2) You may send an RFI and with the information in Table 5.8 and footnote 'b' ask if smaller fillets would be permissible.
3) According to Table 6.1, referenced by your mention of Clause 6.9, you may have a portion of the weld undersize by 1/8" not to exceed 10% of the length of the weld. So it doesn't ALL have to be 5/16".
4) There is nothing I am aware of in D1.1 that states a weld cannot be larger than the thickness of the thinner member.
5) So, if you really want to take the time to ask for a change with the engineer's stamp of approval, sent the RFI (Request For Information).
Have a Great Day, Brent