For a rollover to an IRA, the IRA custodian typically includes in box 2 of the From 5498 the FMV of the shares on the date that the shares are placed in the IRA. As in your case, it usually happens that the value of these shares included in box 2 is different than the value of the shares distributed from the 401(k) because of the change in market value between these two events. Even though the share price may be different on the date that the shares are placed in the IRA than on the date that the shares were distributed from the 401(k), the reportable value of the shares rolled over is the value on the date of distribution, not the value on the date that the shares were placed on the IRA.
If your tax return gets examined, the IRS examiner might question the discrepancy since nothing on the Form 1099-R or Form 5498 explains that the difference is due to a change in the share price. In that case you'll need to provide the explanation. You also have the code-G indicating a direct rollover that would support your explanation indicating that the shares were placed in the IRA.
There's a similar problem where funds are directly rolled over from one 401(k) plan to another because there is no reporting requirement for the receiving 401(k) like Form 5498. The IRS sometimes questions these rollovers, but usually only indirect rollovers reported with code 1, 2 or 7 since they are more likely to trust that a rollover reported with code G was completed.
You can include an explanation with your tax return, but I don't think that there is a good way to do that when e-filing with TurboTax.
