For lightweight stuff the counter sunk head on the bottom of the floor board will be fine, but if you intend to blast about I highly recommend using a pan head bolt with a washer. If you are going to fill the depression anyways why not make it as strong as possible? I pull my auxiliary ten gallon gas tank off my floor regularly. The footmans loop is low profile and fits my web straps perfectly without posing a hazard.
Add a ss teflon insert locking nut on top and you are good to go. I would hate to kick a large ring or an eye nut. I can step on my footmans loop without grief (I ground the bolt flush to the top of the self locking nut).
It's all good, no matter how you go. Much better to tie everything down than try to retrieve it from the sea!