With an employment check by the federal government, it is not uncommon for the government to be able to see your record. Is he supposed to see it? Probably, but I do not know what kind of job you have.
If the file was sealed, the electronic record remains. The file is put in an envelope (sealed). Did you have the record destroyed, too? Maybe you can do so now, which would then trigger an order to the DOJ and CHHRS to remove your record.
As to dropping your charge of arson, can it be lowered? Were you charged with felony arson? There is authority that a judge can entertain a Penal Code section 17(b) motion to reclassify even after probation ends. Talk to an attorney.
It is very possible for the federal government to see certain records that otherwise don't come up in a search. However, I am concerned as to whether your record sealing was a success in the first place. I would have expected you to get some kind of notice, maybe a letter, confirming the sealing or advising you that the sealing was not a success. If you want to know what your record looks like for most people (perhaps not the feds) you can request your rap sheet and read it for yourself.