You are entitled to a step-up in basis for assets to which step-up in basis applies, even for assets held within the trust. However, the issue here is that savings bonds do not get a step-up in basis.
The advisor that told you that you are entitled to a step-up in basis either didn't realize that it was savings bonds that were held in the trust or didn't know this rule.
The sale of your home and most other assets will be "stepped up" to the value of the assets on the date of death (unless an "alternate valuation date" is set, but this is not very common).
There is more information about what happens when a savings bond owner dies HERE.
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