It sounds odd a single ticket was not sold as totally the LATAM codeshare unless the TA saw a huge savings with WS on the one leg and LATAM on the other or the OP wanted WS dollars to any extent possible on the R/T. But at the end of the day and setting aside the oddball non-reciprocal interline agreement if that's the case, the OP's flight is also a LATAM codeshare so there won't be any difficulty with the concept (e.g. baggage handlers seeing luggage go to LATAM in LAX) of treating it like LATAM. I would have done it all LATAM myself to prevent this sort of concern.

Here's the current interline info

Interline Agreements

(WS)

E-Ticket Interline Agreements

AA AF AM AS BA DL PB QF UA US 5T 7F 9M

Baggage Interline Agreements

MAY CHECK BAGGAGE TO AA AF AM AS AT BA CA CI CX CZ DE DL EI FJ HR HU JL KA KE LO MF NZ PB PR PS QF QR TP UA VA 5T 7F 9M 9W

(LA)

E-Ticket Interline Agreements

AA AC AF AI AM AS AT AV AY AZ BA B6 CA CI CM CX CZ DL DT EK ET EW EY FM GA HA HR HU IB IG JJ JL JQ KA KE KL LG LH LO LR LX LY MF MH MS MU NH NU NZ OK OS OU OZ PZ QF QR RJ SA SK SN SQ SU S7 TA TG TK TN UA UL UX VT VX VY WS XL ZP 2Z 4M 4O 9B 9W

Baggage Interline Agreements

MAY CHECK BAGGAGE TO AA AC AF AI AM AS AT AV AY AZ BA BE B6 CA CI CM CX CZ DL DT EK ET EW EY FM GA HA HG HR HU IB IG IZ JC JJ JL JO JQ KA KE KL KX LA LG LH LO LP LR LX LY MD MF MH MS MU MX NH NU NZ OK OS OU OZ O6 PU PZ QF QR SA SK SN SQ SU S7 TA TG TK TN T0 UA UL VW VX VY WS XL ZP 2A 2K 2Z 4M 4O 9W