There is no such thing in D&D 5e as "physical" damage. Damage reduces your hit points and comes in a variety of types but there is no mechanical difference between say bludgeoning and psychic damage - both cause loss of hit points.
"damage from spells" needs to be given a simple reading. Damage from a spell is the damage that is listed in the spell's description- that is the damage from the spell. Specifically, the damage from Bones of the Earth is damage from spells.
Examples of things that are not damage from spells is the damage done by summoned creatures, the damage done by a polymorphed creature or the damage done by teleporting someone 3 miles above the earth and letting them fall. This is because none of these sources of damage come from the spell description.
Rules as written, no, auras don't require line of effect.
There is a general rule, regarding the area targeted by spells, on page 204 of the PHB:
A spell's effect expands in straight lines from the point of origin. If no unblocked straight line extends from the point of origin to a location within the area of effect, that location isn't included in the spell's area. To block one of these imaginary lines, an obstruction must provide total cover, as explained in chapter 9.
However, many auras are not spells - and even spells that cause auras do not have an "area" parameter described as an aura - there is no such thing. The target of these spells is typically a single creature or object that is invested with the aura, which is then described separately in the spell's description; the aura is not subject to the area rules which define who is targeted by a spell, and the creatures who may end up affected by an aura are not the spell's targets.
An "aura" seems to be an entirely separate concept which is not specially defined anywhere else. Thus there are no general rules describing how auras work and certainly no rule that states auras require line of effect, so the effect of an aura is only blocked by cover if the description of the aura states it is. Usually, the only criteria given is that the subject is within a certain distance of the aura's source, and there is no mention of any obstacles that might be between them - though there are many auras that specify that the subject must be able to see/look at the source of the aura as well, so line of sight is necessarily required in those cases.
The Antipathy (Sympathy) spell is a particularly unusual case which specifies an aura which takes effect if the creature is within 60ft of the source or can see it, giving it an astonishingly large effective range (and suggesting that line of sight is not at all required for the effect if you're within the 60ft radius).
DM discretion obviously applies.
Any given DM, of course, is free to rule differently. The spellcasting system establishes that line of effect is required as a general rule when targeting spells and affecting areas, so it's not wildly unreasonable to decide that other supernatural effects are subject to similar restrictions. Personally, if it came up, I would be tempted to houserule that the same rules that Detect X spells impose on their ability to detect "auras" apply to the propagation of other auras:
The spell can penetrate most barriers, but it is blocked by 1 foot of stone, 1 inch of common metal, a thin sheet of lead, or 3 feet of wood or dirt.
This makes for a more interesting tactical experience as regards positioning - wooden or shallow dirt walls would not usually offer any cover from an hostile aura or impede benefiting from a friendly one, but stone or metal walls would.
Best Answer
Yes, the two different Paladin auras stack
They don't have the same name, so they both apply to whomever is within the aura(s) area of effect. The Paladin's aura is a class feature (see below)
There was an errata to the DMG that says this:
The bold and italics I added for emphasis.