Yes, Box 7 of Form 5498 reports the type of IRA, whereas certain other boxes are used to report the type of contribution. Normally, the type of IRA would correspond to the type of contribution, and a personal (non SEP contribution) can clearly be made to a SEP IRA. In such a situation Box 7 would show SEP but the contribution would be reported in Box 1.
However, what about when a SEP contribution is made to a TIRA? Box 7? The 5498 Inst state:
Box 7. Checkboxes
Check the appropriate box.
IRA. Check “IRA” if you are filing Form 5498 to report
information about a traditional IRA account.
SEP. Check “SEP” if you are filing Form 5498 to report
information about a SEP IRA. If you do not know whether the
account is a SEP IRA, check the “IRA” box.
The custodian not knowing what type of account a SEP contribution is going to is a rare situation, possibly involving a prototype SEP or other SEP which is not an IRS form 5305 SEP. I guess the custodian should only show the type of IRA as a SEP when they know for sure that it is a SEP. I think there are situations where a SEP Contribution can be made to a non SEP IRA. For taxpayer purposes, I would just focus on the contribution type, not Box 7.
I do not see any such conflicts for recharacterized contributions since no recharacterizations from TIRA to SEP or vice versa are allowed.