It's not only about "additional overheads like VXLAN" - the path MTU can potentially decrease at any hop. The ubiquity of Ethernet lets people forget about that frequently.
Setting IPv4's Don't Fragment flag with TCP segments is a good approach as it's much more efficient (both bandwidth and processing wise) and it also provides a smoother flow to adapt the MSS to the path MTU instead of relying on in-path fragmentation.
However, setting the DF bit requires proper path MTU discovery, and if the decreasing-MTU hop (router) doesn't return a proper Fragmentation required, and DF flag set ICMP message then that might prove difficult. The TCP stack would first need to try a normal retransmit (could be any kind of packet loss) and then (re)discover the path MTU - either by relying on ICMP or by simply probing. Since the actual path may change for any transmitted packet, so can the path MTU. However, the MSS is only dynamically decreased, not increased.
will the packet be dropped if network MTU is set to 1500 and MSS derived in server / client will be 1460. (Considering we have additional overhead - VXLAN)
Yes, any additional overhead or other situation lowering the in-path MTU below the current packet's size makes the router drop the packet when fragmentation isn't possible (IPv4 with DF flag, or IPv6). The router absolutely needs to return a Fragmentation required, and DF flag set to the source but unfortunately that isn't always the case.
PMTUD usually relies on Fragmentation required messaging, but may also require dealing with black hole connections. For instance, a double retransmit without ACK may trigger decreasing the used MSS MMS_S by some amount. If subsequent retransmits are then successfully ACKed, the MMS_S (maximum message size for send, effective MSS derived from path MTU) may decrease permanently for that connection (and could even by cached for that destination). Alternatively, extensive probing may be used - see RFC 4821. Btw, PMTUD has become mandatory for IPv6.