Lo and behold our house's value is identical to what it was last year even though our recent valuation (also done as a refi through Chris a few months back) doesn't match that number...like he said those numbers don't matter.

I just felt handing over all that it entails to list the property, show the property, verify an applicant, do a walk through, obtain a security deposit that it was worth it to hand that over for a one time fee of 75% of my first month’s rent and then take back over once the tenant is in place.

Sometimes its trial and error.Lastly, make SURE, you tie your payment schedule to significant deliverables to make sure the value matches your cash outlay

Is the downpayment a sort of security deposit for the loan? 

What are the best and worst online programs you have used to help manage your properties, receive rent, charge late fees, collect deposits, receive maintenance requests, update leases, etc.

The real estate world is littered with former investors that got worked up over these situations about fairness, minor repairs, petty spats with tenants, security deposits, etc.

That answer has to match the facts of your deal.

Lease and security deposit?

This is where they will use gross deposits as a calculation for monthly income. 

Rent Roll showing current rent rate, deposit, lease term, concessions, unit type & arrearage.